OSCR

Transcriptional and cellular maturation of the chick spinal cord in the context of distinct neuromuscular circuits.

Code ↔ Paper

15 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 15 matches
  1. [1] § STAR★Methods › Method details › Revigo ↔ scripts/REVIGO_Gg_devel_modules.R, lines 33–92 · score 0.85 · GalGal, parameter Tiny, p.val, GO terms, Revigo, database
  2. [2] § STAR★Methods › Method details › PCA of all samples ↔ scripts/Fig_1_plots.R, lines 115–196 · score 0.85 · DESeqDataSetFromMatrix, AggregateExpression, DESeq2, DDS, vst, pseudobulk
  3. [3] § STAR★Methods › Method details › Seurat objects ↔ markdown/Gg_D05_ctrl.Rmd, lines 334–407 · score 0.83 · terminal sister, latent.vars, min.pct, Find Clusters, variable genes, PCA space
  4. [4] § STAR★Methods › Method details › Seurat objects ↔ markdown/Gg_D07_ctrl.Rmd, lines 333–406 · score 0.83 · terminal sister, latent.vars, min.pct, Find Clusters, variable genes, PCA space
  5. [5] § STAR★Methods › Method details › scWGCNA ↔ markdown/Gg_int_scWGCNA_module_analysis.Rmd, lines 69–210 · score 0.75 · sc.MEList, averageExpr, VlnPlot, pheatmap, WGCNA, eigengenes
  6. [6] § STAR★Methods › Method details › scWGCNA ↔ R/plotting.R, lines 68–138 · score 0.72 · scW.p.expression, sc.MEList, averageExpr, scWGCNA, Seurat, position
  7. [7] § Results › Cell type repertoires in spinal cord segments innervating wings and legs ↔ scripts/Fig_4_plots.R, lines 204–264 · score 0.63 · HOX gene, HOXD10, HOXD3, HOXD8, HOXD9, HOXA11
  8. [8] § STAR★Methods › Method details › Integration ↔ scripts/Fig_5_plots.R, lines 128–209 · score 0.59 · B10int, Poly10int, L10int, vars, cc, DE
  9. [9] § STAR★Methods › Method details › scWGCNA ↔ markdown/scWGCNA_Gg_ctrl_int.Rmd, lines 130–226 · score 0.55 · KEGG pathways, limma, scWGCNA, goana, kegga, GOterm
  10. [10] § STAR★Methods › Method details › scWGCNA ↔ markdown/scWGCNA_Gg_devel_int.Rmd, lines 130–226 · score 0.55 · KEGG pathways, limma, scWGCNA, goana, kegga, GOterm
  11. [11] § Results › Cell fate- and cell state-defining gene co-expression dynamics during spinal cord maturation ↔ scripts/REVIGO_Gg_devel_modules.R, lines 33–92 · score 0.55 · GO terms, translation, DNA, signaling, production, regulatory
  12. [12] § STAR★Methods › Method details › QC and filtering ↔ markdown/QCfilter_D5_ctrl.Rmd, lines 49–131 · score 0.53 · median absolute, removing cells, mapping, mitochondrial, UMI, thresholds
  13. [13] § STAR★Methods › Method details › QC and filtering ↔ markdown/QCfilter_D7_ctrl.Rmd, lines 49–131 · score 0.53 · median absolute, removing cells, mapping, mitochondrial, UMI, thresholds
  14. [14] § STAR★Methods › Method details › GSI Pseudo bulk correlation ↔ markdown/heatmap_spearman_devel.Rmd, lines 45–101 · score 0.53 · AverageExpression, bulk, spearman, GSI, Heatmaps, slot
  15. [15] § STAR★Methods › Method details › GSI Pseudo bulk correlation ↔ markdown/heatmap_spearman_ctrl_lumb_poly_int.Rmd, lines 44–100 · score 0.52 · AverageExpression, bulk, spearman, GSI, Heatmaps, slot

Paper

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The authors' code

R · 326 lines · 47 KB · no license · 2 matches

  1. # revigo
  3. setwd("~/spinal_cord_paper/")
  5. # Devel GOterms
  6. dev_GO <- read.csv("tables/Supp_table_3.csv") %>%
  7. filter(sample == "Devel") %>%
  8. filter(P.DE < 0.01) %>%
  9. select(c(ID, P.DE))
  12. write.table(dev_GO,
  13. file = "output/Gg_devel_int_revigo_GOTerms.tsv",
  14. sep = "\t",
  15. quote = FALSE,
  16. row.names = FALSE)
  18. # The table was pasted to http://revigo.irb.hr/. The code below is adapted from the scatterplot export file
  20. # A plotting R script produced by the Revigo server at http://revigo.irb.hr/
  21. # If you found Revigo useful in your work, please cite the following reference:
  22. # Supek F et al. "REVIGO summarizes and visualizes long lists of Gene Ontology
  23. # terms" PLoS ONE 2011. doi:10.1371/journal.pone.0021800
  25. library(ggplot2)
  26. library(tidyverse)
  27. library(scales)
  28. library(plotly)
  30. # --------------------------------------------------------------------------
  31. # Here is your data from Revigo. Scroll down for plot configuration options.
  33. # revigo was run with parameter Tiny(0.4) against the GalGal database,
  34. # also the GO terms were filtered to p.val < 0.01 to N terms is < 3000 for
  35. # revigo to run
  37. revigo.names <- c("term_ID","description","frequency","plot_X","plot_Y","log_size","value","UserValue_0","uniqueness","dispensability")
  38. revigo.data <- rbind(c("GO:0000053","argininosuccinate metabolic process",0.008972633467922835,-0.3172071538986599,7.788500661564704,0.3010299956639812,-2.5991764319797968,0.00251665433012571,0.9380844099468589,0.20850829),
  39. c("GO:0001503","ossification",0.6998654104979811,3.8989779400864966,5.32352065819406,1.8976270912904414,-2.182726278381996,0.00656558943569559,0.9037529246081665,0.36942063),
  40. c("GO:0001662","behavioral fear response",0.06280843427545985,3.728108978477911,2.690967029711254,0.9030899869919435,-2.916159785640011,0.00121294250251457,0.8867832171413306,0.3953544),
  41. c("GO:0001765","membrane raft assembly",0.053835800807537006,6.059108557074353,0.5470164538514686,0.8450980400142568,-3.219412058356641,0.000603375875018884,0.9552389757325513,0.38649352),
  42. c("GO:0001816","cytokine production",0.026917900403768503,2.4802574241148445,5.4118608881729005,0.6020599913279624,-3.0100227602713225,0.000977186007775804,0.8794182814752842,0.32423957),
  43. c("GO:0002076","osteoblast development",0.026917900403768503,4.940978586907927,4.770736406190018,0.6020599913279624,-2.3531793093093913,0.00443425526842756,0.8683942875126793,0.37604251),
  44. c("GO:0002376","immune system process",5.033647375504711,-5.017725088616433,-5.895905481921542,2.749736315569061,-2.0966166187484028,0.00800540634795397,1,-0),
  45. c("GO:0002682","regulation of immune system process",2.781516375056079,-1.5190369201482146,-7.339825191691662,2.4927603890268375,-2.0417225138931174,0.0090840075417053,0.9300516825628105,0.1083849),
  46. c("GO:0005979","regulation of glycogen biosynthetic process",0.026917900403768503,3.5243835408716757,-6.366421208920479,0.6020599913279624,-2.292513735351047,0.00509901470760588,0.9192035203412366,0.22938338),
  47. c("GO:0006091","generation of precursor metabolites and energy",1.5074024226110363,0.11600941495717051,6.331291715861255,2.2278867046136734,-2.424283514044855,0.00376457961265042,0.9469802346909583,0.27068147),
  48. c("GO:0006112","energy reserve metabolic process",0.2691790040376851,0.3108767126919522,7.2413813161565,1.4913616938342726,-2.0713721479709735,0.00848453121954196,0.9528111972326937,0.22216841),
  49. c("GO:0006139","nucleobase-containing compound metabolic process",14.212651413189773,-0.6542147246875359,5.76522344981138,3.2000292665537704,-2.688722172171583,0.0020477542116603,0.9500585651178166,0.3489153),
  50. c("GO:0006281","DNA repair",2.584118438761777,1.7736978372825267,2.7839051461067634,2.4608978427565478,-4.34417030998722,4.52720009470973E-05,0.8783631879965197,0.28206882),
  51. c("GO:0006412","translation",2.4854194706146258,0.40279300108741944,6.366689967326808,2.444044795918076,-16.180932908364106,6.59275735062751E-17,0.9171736313967129,0),
  52. c("GO:0006518","peptide metabolic process",0.19739793629430236,-3.289862022194802,6.370433608295669,1.3617278360175928,-14.961760156252646,1.09204326245537E-15,0.9725645560696133,0.11725724),
  53. c("GO:0006575","cellular modified amino acid metabolic process",0.5473306415432929,-0.5586236612097621,7.065743064456107,1.792391689498254,-2.749927434308268,0.00177857656522324,0.946016839670993,0.30478929),
  54. c("GO:0006793","phosphorus metabolic process",5.060565275908479,-0.04897395837638205,6.032155517601148,2.7520484478194387,-3.131957275364511,0.000737976826584674,0.9394013514202455,0.31976788),
  55. c("GO:0006809","nitric oxide biosynthetic process",0.07178106774338268,2.0412421007885357,7.258348019938713,0.9542425094393249,-2.2564943108979376,0.00553994801024404,0.9616319528211146,0.24407785),
  56. c("GO:0006836","neurotransmitter transport",0.3858232391206819,-7.09202702125211,1.1106338975167342,1.6434526764861874,-2.249009307780715,0.00563625576097328,0.968008096404587,0.26709096),
  57. c("GO:0006950","response to stress",9.089277703005832,5.931495478764736,-2.7240000247670824,3.0060379549973173,-2.273476046845113,0.00532750606934138,0.9607323268683589,0.33645935),
  58. c("GO:0007017","microtubule-based process",2.772543741588156,-5.593979047393095,-5.402909153789744,2.4913616938342726,-5.935511706252965,1.1600809461582E-06,0.9910965039592073,0.01645451),
  59. c("GO:0007049","cell cycle",3.0148048452220726,-6.085763438070793,-4.789180460147308,2.5276299008713385,-4.373607578648739,4.23050703272745E-05,0.991013976605518,0.01722642),
  60. c("GO:0007059","chromosome segregation",0.9600717810677433,-7.500470100683699,-1.8904427037749545,2.03342375548695,-8.059604408742139,8.71757296909308E-09,0.9540802809222686,0.01436232),
  61. c("GO:0007154","cell communication",22.987886944818303,-7.290621818453593,-2.5757104960145485,3.408748606184244,-2.4376332583046456,0.00365062094930861,0.9883567143977848,0.03942097),
  62. c("GO:0007155","cell adhesion",3.54419021982952,-6.707938851184552,-3.7618512718005337,2.597695185925512,-3.5634032458179723,0.00027327301866432,0.9908499639222146,0.01763672),
  63. c("GO:0007156","homophilic cell adhesion via plasma membrane adhesion molecules",0.9959623149394347,-6.3715192063800465,-4.2286006528036655,2.0492180226701815,-2.9140088310848897,0.00121896481184691,0.9848652961762715,0.0144258),
  64. c("GO:0007166","cell surface receptor signaling pathway",7.662628981606101,3.7770382709980206,-3.4863381977270445,2.931966114728173,-3.2658712991909566,0.00054216153322101,0.8695504726979314,0.3732028),
  65. c("GO:0007167","enzyme-linked receptor protein signaling pathway",2.2611036339165542,4.586806969727327,-3.3542437538668652,2.403120521175818,-5.698742297397589,2.00104890415785E-06,0.8791647756041004,0.18447136),
  66. c("GO:0007218","neuropeptide signaling pathway",0.6729475100942126,5.158362505412217,-3.2586412285144783,1.8808135922807914,-2.3760191055364976,0.00420708120133746,0.8986803579058535,0.26993373),
  67. c("GO:0007267","cell-cell signaling",2.243158366980709,1.9530873201989267,-6.955400486844629,2.399673721481038,-2.442383170127013,0.00361091137910512,0.9143772289381202,0.29985434),
  68. c("GO:0007585","respiratory gaseous exchange by respiratory system",0.07178106774338268,4.102424738143457,5.907799543807608,0.9542425094393249,-2.352504098638382,0.00444115470022211,0.9193162005027088,0.29073541),
  69. c("GO:0007605","sensory perception of sound",0.3050695379093764,3.9997881982653656,5.602715682066253,1.5440680443502757,-3.504280643601595,0.000313126163105139,0.9029949091521207,0.33623956),
  70. c("GO:0007610","behavior",1.1843876177658144,3.6962945547521073,4.700136654832207,2.123851640967086,-3.52931828110701,0.000295584542410647,0.8992449188407393,0.39405858),
  71. c("GO:0008037","cell recognition",0.2960969044414536,-5.284708809119931,5.745031715367892,1.5314789170422551,-2.8339882442883297,0.00146558751171332,0.992836182054941,0.0125871),
  72. c("GO:0008150","biological_process",100,-6.028826535847033,4.903562396446329,4.047119038720181,-2.1738333343262743,0.0067014173493856,1,-0),
  73. c("GO:0008152","metabolic process",38.70794078061911,-6.343998300195812,4.532369332714066,3.6349808000512285,-3.9752767036133276,0.00010585790539726,1,-0),
  74. c("GO:0008283","cell population proliferation",1.5791834903544189,-5.3255596550651605,4.545188213177758,2.247973266361807,-3.425932592434028,0.000375031206943235,0.9916123975578104,0.01527364),
  75. c("GO:0009056","catabolic process",6.576940331987438,-1.4927842574140233,6.039386684244208,2.8656960599160706,-5.14368988812715,7.18307021765788E-06,0.9606207715691893,0.18133063),
  76. c("GO:0009058","biosynthetic process",19.18349035441902,-1.0029142183121167,6.1045936053935055,3.330210784571528,-3.0588517038303626,0.000873269508062361,0.9543290910607686,0.3833991),
  77. c("GO:0009132","nucleoside diphosphate metabolic process",0.4127411395244504,0.6271338823830129,5.289228702378293,1.6720978579357175,-3.896595589893784,0.000126883283869702,0.9048293593043654,0.36600995),
  78. c("GO:0009308","amine metabolic process",0.33198743831314487,-1.9058667429481806,7.3232561500067845,1.5797835966168101,-2.114091155397609,0.00768969022086077,0.9622851561404545,0.28858293),
  79. c("GO:0009605","response to external stimulus",3.9030955585464335,6.1183465226561955,-2.4210265077981306,2.639486489268586,-2.952515819729354,0.00111553751573668,0.9644984017183205,0.24281258),
  80. c("GO:0009628","response to abiotic stimulus",2.2700762673844777,6.481313832852869,-2.5402359258761074,2.404833716619938,-3.7496149643840058,0.000177985669123048,0.9665440133480189,0.21312789),
  81. c("GO:0009636","response to toxic substance",0.6998654104979811,6.476329417581519,-3.126209096167159,1.8976270912904414,-9.163569784065794,6.86167613567806E-10,0.9551277563337668,-0),
  82. c("GO:0009719","response to endogenous stimulus",3.3198743831314492,6.2724423427735765,-2.768292853366057,2.569373909615046,-3.3740573044201376,0.000422612847538221,0.9651359401041416,0.23261326),
  83. c("GO:0009987","cellular process",77.03903095558546,-5.704911517347351,5.3547558908348645,3.9338414628987213,-2.2806948421381685,0.00523968474736439,1,-0),
  84. c("GO:0010332","response to gamma radiation",0.13458950201884254,7.083827275193193,-2.485496700012384,1.2041199826559248,-3.6707671088765497,0.000213418906870652,0.9650810786296252,0.13949809),
  85. c("GO:0010608","post-transcriptional regulation of gene expression",2.108568864961866,2.438776032989438,-5.543582909143748,2.3729120029701067,-2.7112062877833654,0.00194443626439229,0.8911242001087634,0.33596019),
  86. c("GO:0010646","regulation of cell communication",8.353521758636159,0.01427178230486,-5.366173014927443,2.9694159123539814,-4.216160536566817,6.07910246262195E-05,0.9146036538001816,0.16342823),
  87. c("GO:0015669","gas transport",0.14356213548676536,-6.801584297738732,1.9512328240030845,1.2304489213782739,-11.597456467549137,2.52664096078475E-12,0.9706122608119223,0.21103552),
  88. c("GO:0015671","oxygen transport",0.11664423508299686,-7.100770782191045,1.7282504082507522,1.146128035678238,-12.022727858059168,9.49012956984251E-13,0.9711050347058221,-0),
  89. c("GO:0015698","inorganic anion transport",0.924181247196052,-6.295903653669438,1.5179289023125229,2.0170333392987803,-3.398601634510383,0.00039939108402722,0.9652767910681459,0.29202176),
  90. c("GO:0015711","organic anion transport",1.3279497532525795,-6.329986818802838,1.264670803179591,2.173186268412274,-2.3239564622581685,0.00474289530096664,0.9639966592659742,0.3378564),
  91. c("GO:0015718","monocarboxylic acid transport",0.5652759084791386,-6.955030352752554,1.3937252016906891,1.806179973983887,-3.176931286512313,0.000665378423151395,0.9647014842134686,0.27744747),
  92. c("GO:0015837","amine transport",0.3351560065895294,-6.320014061045554,1.9460060172610412,1.662757831681574,-2.1583199935162187,0.0069451240373796,0.9657938702050716,0.35571982),
  93. c("GO:0015846","polyamine transport",0.008972633467922835,-6.30883466820134,2.555274702098411,0.3010299956639812,-2.345325514011268,0.00451517394522571,0.9739707179357351,0.28661964),
  94. c("GO:0016126","sterol biosynthetic process",0.19739793629430236,1.86708755341016,6.711069592705926,1.3617278360175928,-7.03671971324531,9.18925465036114E-08,0.9338109463992882,0.2689618),
  95. c("GO:0016241","regulation of macroautophagy",0.2781516375056079,3.349328852603019,-5.231776715163843,1.505149978319906,-2.024940644938655,0.0094418990997821,0.9116938298118616,0.25184481),
  96. c("GO:0019222","regulation of metabolic process",20.87931807985644,-0.34299226765185176,-6.0189927012945805,3.3669829759778507,-4.572538880989199,2.67584602258092E-05,0.9094721180355673,0.20041419),
  97. c("GO:0019827","stem cell population maintenance",0.2691790040376851,4.680683255859526,4.606724099378203,1.4913616938342726,-2.1356420391631517,0.00731741962538549,0.8739852870435234,0.36598448),
  98. c("GO:0022408","negative regulation of cell-cell adhesion",0.2871242709735307,1.1978950820976189,-1.7322211093389732,1.5185139398778875,-4.210154621115685,6.16375515679917E-05,0.8956935490979677,0.3748095),
  99. c("GO:0022411","cellular component disassembly",0.924181247196052,7.230263490708368,0.6051682192406046,2.0170333392987803,-2.41935277278684,0.00380756413362149,0.9527629853358722,0.29350498),
  100. c("GO:0022414","reproductive process",2.4854194706146258,-4.746982761086394,5.160247121582966,2.444044795918076,-2.0775662180211714,0.00836438052124269,1,-0),
  101. c("GO:0023051","regulation of signaling",8.362494392104082,-0.35648718609809016,-6.838808049953837,2.9698816437465,-4.793197090790219,1.60991486052121E-05,0.9202541924570002,0.14672026),
  102. c("GO:0023052","signaling",22.88021534320323,-0.05939928234839619,-5.916683131473479,3.40671045860979,-2.5017940771915175,0.00314924118793806,0.9082114594286667,0.35482737),
  103. c("GO:0030001","metal ion transport",3.436518618214446,-6.634388631125756,1.316092154823297,2.584331224367531,-2.5569264136404293,0.0027737900526464,0.9554360418307409,0.3815227),
  104. c("GO:0030003","intracellular monoatomic cation homeostasis",1.2741139524450427,-2.663542156556512,0.9396788131632651,2.155336037465062,-2.9177695115857385,0.00120845501521138,0.9790505381845115,-0),
  105. c("GO:0030029","actin filament-based process",1.848362494392104,-1.0328378482553566,0.47063122522044254,2.315970345456918,-2.6692547639992985,0.00214163391629521,0.9914745292855872,0.01558643),
  106. c("GO:0030030","cell projection organization",3.1314490803050696,6.903499821908369,0.7990292888144013,2.5440680443502757,-2.7267454457668627,0.00187609382595741,0.9464656653875199,0.34045356),
  107. c("GO:0030155","regulation of cell adhesion",1.4356213548676535,-2.7086673337058587,-5.923335177716651,2.2068258760318495,-2.0271200232041977,0.0093946364109244,0.9301191431710064,0.12369442),
  108. c("GO:0030198","extracellular matrix organization",0.7357559443696725,7.232241756445026,0.8321301189088411,1.919078092376074,-4.336887208919043,4.60376122828164E-05,0.9522089702751595,0.26896681),
  109. c("GO:0030318","melanocyte differentiation",0.04486316733961417,5.778006163945274,4.680019090955297,0.7781512503836436,-2.1494934520550397,0.00708771992668034,0.8903845921252864,0.39325262),
  110. c("GO:0030335","positive regulation of cell migration",1.0049349484073575,-1.222948286430863,-3.054090694834574,2.0530784434834195,-4.3289694087128385,4.68846406073757E-05,0.8730189554107374,0.30545774),
  111. c("GO:0030513","positive regulation of BMP signaling pathway",0.09869896814715118,-3.4958328849540243,-3.485940596542995,1.0791812460476249,-3.8167903230564386,0.00015247887426028,0.8777722580962023,0.25362121),
  112. c("GO:0031100","animal organ regeneration",0.03589053387169134,6.033881703450454,4.525305945057644,0.6989700043360189,-2.298677211261121,0.00502716093703814,0.8844222727374378,0.3253194),
  113. c("GO:0031128","developmental induction",0.10767160161507401,6.139523339752495,4.26232870192019,1.1139433523068367,-2.0251329573681267,0.00943771900388291,0.8984864228273347,0.33338246),
  114. c("GO:0031399","regulation of protein modification process",1.911170928667564,2.6668669356180774,-5.811572629478384,2.330413773349191,-4.069204988514296,8.52697542795253E-05,0.8873219060816523,0.097988),
  115. c("GO:0032196","transposition",0.008972633467922835,-4.914125392647804,6.151460327239384,0.3010299956639812,-2.625505370702134,0.00236861584011838,0.9944944507687976,0.00920515),
  116. c("GO:0032501","multicellular organismal process",15.791834903544192,-4.43043576130706,4.229357573254735,3.245759355967277,-2.01116629530547,0.00974616376788136,1,-0),
  117. c("GO:0032502","developmental process",13.710183938986093,-2.764980348213169,1.9942165787604187,3.1844074854123203,-2.7578353392713835,0.00174648419875057,1,-0),
  118. c("GO:0032879","regulation of localization",3.894122925078511,-0.7282820220973759,-7.404092352330505,2.6384892569546374,-3.8325014988457697,0.000147061333998574,0.9273408514112016,0.12890231),
  119. c("GO:0032886","regulation of microtubule-based process",0.5024674742036788,-3.8303166236708495,-6.357115128169234,1.7558748556724915,-3.0905775585878943,0.000811750269367026,0.9368453483855395,0.09380172),
  120. c("GO:0032908","regulation of transforming growth factor beta1 production",0.013458950201884251,4.605799550444426,-5.633772846693652,0.3010299956639812,-2.916113603024757,0.00121307149295253,0.9010703016810068,0.20267567),
  121. c("GO:0032989","cellular anatomical entity morphogenesis",0.33198743831314487,7.264238523220654,1.1051187003885699,1.5797835966168101,-2.906261664009575,0.00124090443286901,0.9569859231457623,0.2409858),
  122. c("GO:0033344","cholesterol efflux",0.03589053387169134,-7.180021323305692,0.4646403877990194,0.6989700043360189,-3.3873653408434827,0.000409859172756446,0.9679373372576993,0.32706474),
  123. c("GO:0034248","regulation of amide metabolic process",0.11664423508299686,3.7768939268861863,-6.117928145445432,1.146128035678238,-2.8563637349110427,0.00139199047999832,0.9231895502220611,0.23141184),
  124. c("GO:0034249","negative regulation of amide metabolic process",0.008972633467922835,2.222646470073612,-3.27396231083817,0.3010299956639812,-2.321189365694702,0.00477321101657668,0.9096959587852501,0.26691947),
  125. c("GO:0034330","cell junction organization",1.1484970838941229,6.848975612055368,0.5494831558124952,2.110589710299249,-2.6030743534279415,0.00249416767617394,0.9517549842715589,0.30089351),
  126. c("GO:0034371","chylomicron remodeling",0.008972633467922835,5.344979872604417,2.2378855493272107,0.3010299956639812,-2.352504098638382,0.00444115470022211,0.8600943068713918,0.24339643),
  127. c("GO:0034502","protein localization to chromosome",0.19739793629430236,-6.941955383400253,0.4423723283311288,1.3617278360175928,-4.479282598774884,3.31678561514977E-05,0.9546406043498921,0.19891066),
  128. c("GO:0034587","piRNA processing",0.03589053387169134,1.6311161547961173,0.1389797560746427,0.6989700043360189,-2.3249739633325097,0.00473179626006892,0.8366695996896222,0.35238315),
  129. c("GO:0035092","sperm DNA condensation",0.01794526693584567,6.211437021419597,2.6585510225394615,0.47712125471966244,-2.625505370702134,0.00236861584011838,0.8464614589382532,0.36341843),
  130. c("GO:0035606","peptidyl-cysteine S-trans-nitrosylation",0.008972633467922835,-1.5431103712430871,7.755897637109065,0.3010299956639812,-2.345325514011268,0.00451517394522571,0.9634369622479926,0.26101808),
  131. c("GO:0038162","erythropoietin-mediated signaling pathway",0.008972633467922835,6.090954077608081,-4.137757139426783,0.3010299956639812,-2.750444107310474,0.00177646188008862,0.9101908482812933,0.36191102),
  132. c("GO:0040007","growth",0.9152086137281292,-6.924330871484086,-2.105598991149465,2.012837224705172,-3.888998613956386,0.000129122339452494,1,-0),
  133. c("GO:0040008","regulation of growth",1.0946612830865858,-3.265318114943211,-6.740421099336964,2.089905111439398,-2.4800076302682754,0.00331125303777782,0.9365582946168559,0.09180825),
  134. c("GO:0040011","locomotion",1.0139075818752805,-6.208084782625786,-2.3241152423156266,2.0569048513364727,-2.6264691930761774,0.00236336503983909,1,-0),
  135. c("GO:0040012","regulation of locomotion",2.0188425302826376,-2.3799913329796354,-7.084098913956499,2.3541084391474008,-3.884703547171403,0.00013040566340199,0.9324413890182979,0.10321007),
  136. c("GO:0042044","fluid transport",0.03589053387169134,-5.6373163315530705,1.6089261369464753,0.6989700043360189,-2.0524235216022464,0.00886291284057161,0.9736107840437438,0.19111503),
  137. c("GO:0042058","regulation of epidermal growth factor receptor signaling pathway",0.10767160161507401,-4.723281133838741,-4.1425414756983745,1.1139433523068367,-2.4896275119064404,0.00323871317583019,0.9151286158124494,0.35592951),
  138. c("GO:0042127","regulation of cell population proliferation",3.4096007178106778,0.8807477166542532,-7.188311384355962,2.5809249756756194,-2.1781381069037034,0.0066353203173942,0.9233228289166406,0.14034394),
  139. c("GO:0042221","response to chemical",9.071332436069987,5.770512899828756,-2.5989355762109603,3.0051805125037805,-2.335961193295715,0.00461358797774811,0.9607420956859448,0.28606152),
  140. c("GO:0042254","ribosome biogenesis",1.3279497532525795,6.418592244122582,0.7222750770690355,2.173186268412274,-4.75114462036396,1.77359877291993E-05,0.9434946565731301,0.26443551),
  141. c("GO:0042402","cellular biogenic amine catabolic process",0.026917900403768503,-2.6321852588946593,7.199614454172622,0.6020599913279624,-3.6398945222229724,0.000229142410693225,0.9617326080449887,0.33375601),
  142. c("GO:0042592","homeostatic process",3.3378196500672948,-7.025818037927583,-3.1435937502854143,2.571708831808688,-2.5818051506035924,0.00261935793872994,1,-0),
  143. c("GO:0042744","hydrogen peroxide catabolic process",0.08972633467922835,-0.13557200704216663,4.44156852820987,1.0413926851582251,-12.022727858059168,9.49012956984251E-13,0.9521443574040365,0.19938067),
  144. c("GO:0043043","peptide biosynthetic process",0.026917900403768503,2.670349637191217,7.126606593795612,0.6020599913279624,-16.112953591032095,7.70985852671586E-17,0.9654082333895329,0.22398541),
  145. c("GO:0043062","extracellular structure organization",0.7447285778375954,7.148026959125923,0.3934043096979221,1.9242792860618816,-4.336887208919043,4.60376122828164E-05,0.9537226373495575,0.26932036),
  146. c("GO:0043067","regulation of programmed cell death",3.3647375504710633,-1.372038885373347,-6.678058451230193,2.575187844927661,-2.146030606173601,0.00714445974922166,0.9234374898810818,0.14005527),
  147. c("GO:0043170","macromolecule metabolic process",25.0695379093764,-0.8328421480379379,6.032858343929314,3.446381812222442,-3.526420505680072,0.00029756338763088,0.9523972660164011,0.28342114),
  148. c("GO:0043412","macromolecule modification",5.993719156572454,-0.2569191813637736,5.233396140801866,2.8254261177678233,-2.051769953015093,0.00887626065507753,0.952159336856621,0.32044402),
  149. c("GO:0043491","phosphatidylinositol 3-kinase/protein kinase B signal transduction",0.1525347689546882,5.889259148397093,-3.6614862986228944,1.255272505103306,-2.9678878062876266,0.00107674333880726,0.9074942703459788,0.23093989),
  150. c("GO:0043603","amide metabolic process",1.085688649618663,-2.3787878049735376,5.910524410877204,2.0863598306747484,-14.060737725233867,8.69485361640259E-15,0.9678729202713007,0.1415821),
  151. c("GO:0043604","amide biosynthetic process",0.48452220726783307,1.5507642738122125,6.842215417509837,1.7403626894942439,-15.29937736395018,5.01906287295365E-16,0.9535055203944072,0.29572365),
  152. c("GO:0043954","cellular component maintenance",0.10767160161507401,7.043997411172709,-0.019972776031069086,1.1139433523068367,-2.4492092172781073,0.00355460037789025,0.9608230308134824,0.21819089),
  153. c("GO:0044087","regulation of cellular component biogenesis",2.126514131897712,-2.093018054241429,-6.375741322297223,2.376576957056512,-2.766727846905551,0.00171108724169261,0.9271967656585809,0.13073917),
  154. c("GO:0044281","small molecule metabolic process",6.846119336025123,-1.3211855291193435,5.510997927910774,2.8830933585756897,-2.4501806518541938,0.00354665829524814,0.9604188173964758,0.28621786),
  155. c("GO:0044341","sodium-dependent phosphate transport",0.01794526693584567,-6.837221027209023,2.448135977570065,0.47712125471966244,-2.5991764319797968,0.00251665433012571,0.973849027889674,0.1825015),
  156. c("GO:0045229","external encapsulating structure organization",0.7357559443696725,6.85427204840951,1.1264377907885563,1.919078092376074,-4.336887208919043,4.60376122828164E-05,0.9537753370259618,0.26896681),
  157. c("GO:0045292","mRNA cis splicing, via spliceosome",0.11664423508299686,1.2385919917833432,5.958261653800469,1.146128035678238,-2.2564943108979376,0.00553994801024404,0.9314367663239723,0.39791175),
  158. c("GO:0046149","pigment catabolic process",0.01794526693584567,-4.381618904352118,6.373580479103162,0.47712125471966244,-2.5991764319797968,0.00251665433012571,0.975585233933008,0.09443556),
  159. c("GO:0046320","regulation of fatty acid oxidation",0.03589053387169134,4.170660367190641,-5.98635391041802,0.6989700043360189,-2.0892626638637988,0.00814211695040723,0.9114562429749803,0.23493342),
  160. c("GO:0046348","amino sugar catabolic process",0.053835800807537006,-3.5034024986971435,5.4075970235707125,0.8450980400142568,-2.750444107310474,0.00177646188008862,0.9592948159437408,0.34966329),
  161. c("GO:0046379","extracellular polysaccharide metabolic process",0.01794526693584567,0.8062247211841312,2.9022006909886167,0.47712125471966244,-2.0524235216022464,0.00886291284057161,0.9604154491477993,0.16828699),
  162. c("GO:0046626","regulation of insulin receptor signaling pathway",0.14356213548676536,-4.462561828760436,-4.121790733227463,1.2304489213782739,-2.167928619224323,0.00679315275911407,0.9147150664683745,0.37016158),
  163. c("GO:0046903","secretion",1.5432929564827276,-6.618453263468604,1.5274867845284508,2.2380461031287955,-2.4800076302682754,0.00331125303777782,0.9634368796309285,0.34408076),
  164. c("GO:0048015","phosphatidylinositol-mediated signaling",0.09869896814715118,6.104033799682883,-3.743429704803496,1.0791812460476249,-2.8757902127548944,0.00133109725320305,0.9109709061918173,0.39694562),
  165. c("GO:0048169","regulation of long-term neuronal synaptic plasticity",0.04486316733961417,-4.486541549888148,-2.9310285489579617,0.7781512503836436,-2.550871752405228,0.00281273131014059,0.9108782240785239,0.39867552),
  166. c("GO:0048263","determination of dorsal identity",0.03589053387169134,4.727456374040607,4.310659145211302,0.6989700043360189,-4.091249096200232,8.10496052182912E-05,0.8652702378557511,0.37588095),
  167. c("GO:0048518","positive regulation of biological process",14.975325257963213,0.09026760554941138,-6.216628688067315,3.2227164711475833,-3.4604699685768523,0.000346361834668944,0.9137439790533717,0.23411253),
  168. c("GO:0048519","negative regulation of biological process",12.489905787348587,-0.5141197624926037,-6.391740150842963,3.1439511164239633,-4.521323455106473,3.01076282425455E-05,0.9158940777597454,0.22246147),
  169. c("GO:0048583","regulation of response to stimulus",9.232839838492596,0.3267996418553851,-6.583628509974536,3.012837224705172,-3.041761096973433,0.000908320054682333,0.9192245339668739,0.20543924),
  170. c("GO:0048699","generation of neurons",3.167339614176761,4.893383804335139,4.5568774810321235,2.5490032620257876,-4.86261581661568,1.37209500519312E-05,0.7893165233532494,0.01702138),
  171. c("GO:0048870","cell motility",2.4405563032750113,-6.338439637449663,-3.169329237333677,2.436162647040756,-2.262285885394057,0.00546655994208939,0.9912191446296256,0.01617121),
  172. c("GO:0050793","regulation of developmental process",5.275908479138628,-0.021279630147529725,-7.337113677710782,2.7701152947871015,-4.04292421274,9.05890671020322E-05,0.9246932836503233,0.14958081),
  173. c("GO:0050794","regulation of cellular process",44.42350829968596,-0.28082293556965904,-5.736009833192543,3.6947806360120614,-3.172936813439649,0.000671526547849404,0.8977453661336972,0.34117134),
  174. c("GO:0050808","synapse organization",0.6280843427545985,6.6918644150432005,0.3229845751491965,1.8512583487190752,-9.800866060893647,1.58173578116052E-10,0.9502947113176778,0.01366701),
  175. c("GO:0050896","response to stimulus",31.027366532077167,-3.647625479615396,3.1484295105148212,3.5389505620143615,-2.6305744689429145,0.00234113000466472,1,-0),
  176. c("GO:0051052","regulation of DNA metabolic process",0.8434275459847466,3.0448297049585102,-5.730703397094402,1.9777236052888478,-2.825386873234538,0.00149490339007513,0.9031064508264708,0.31986334),
  177. c("GO:0051128","regulation of cellular component organization",4.74652310453118,-1.1684056270760468,-5.903062876785914,2.724275869600789,-5.021375358335117,9.51973023302065E-06,0.9203350023303938,0.12238582),
  178. c("GO:0051129","negative regulation of cellular component organization",1.3279497532525795,0.8066390569132406,-2.7369413315493922,2.173186268412274,-6.663346926774985,2.17096625645786E-07,0.8624546592347015,-0),
  179. c("GO:0051174","regulation of phosphorus metabolic process",1.6778824585015704,2.5698779177383253,-5.406938196060873,2.27415784926368,-3.889807930924398,0.000128881941300426,0.8959137542873105,0.30810218),
  180. c("GO:0051179","localization",19.93719156572454,-1.5351318801675493,1.4366783633634512,3.3469394626989906,-2.439637744219323,0.00363381033509024,1,-0),
  181. c("GO:0051239","regulation of multicellular organismal process",5.895020188425303,0.40887100242979657,-7.138110148396136,2.8182258936139557,-4.100722408881249,7.9300804116138E-05,0.9236733559498745,0.15270497),
  182. c("GO:0051246","regulation of protein metabolic process",4.378645132346343,2.2261329362643445,-5.718914586665845,2.6893088591236203,-3.628807609771025,0.000235067392672728,0.8865980946763284,0.39421136),
  183. c("GO:0051301","cell division",1.6689098250336474,0.8684481733304628,1.0588383694061398,2.271841606536499,-6.695502202426091,2.01603374677995E-07,0.9915645228702643,0.01538203),
  184. c("GO:0051336","regulation of hydrolase activity",0.2691790040376851,-2.716696480171995,-0.00202826643378135,1.4913616938342726,-4.52822499020354,2.96329582946618E-05,0.9065409509276463,0.07342922),
  185. c("GO:0051383","kinetochore organization",0.1256168685509197,7.032705836497524,1.4573865283216105,1.1760912590556813,-9.742432095916705,1.8095388184514E-10,0.9491366138416267,0.22105339),
  186. c("GO:0051481","negative regulation of cytosolic calcium ion concentration",0.01794526693584567,-4.652909388258098,-1.860809203722209,0.47712125471966244,-2.9545640899663668,0.00111028867505547,0.9375692567614452,0.37031736),
  187. c("GO:0051640","organelle localization",1.256168685509197,-6.578746970703648,0.769228329618589,2.1492191126553797,-3.7827563697249666,0.000164908723612525,0.9661566200913696,0.28527543),
  188. c("GO:0051656","establishment of organelle localization",0.9331538806639749,-6.839192881133261,0.9733798026257884,2.0211892990699383,-4.28464719956424,5.19221658938489E-05,0.9568723181127156,0.26322482),
  189. c("GO:0051674","localization of cell",0.008972633467922835,-6.912962023021028,-0.2185730429998074,0.3010299956639812,-2.2428191007218463,0.00571716727669825,0.9724729919241435,0.16065652),
  190. c("GO:0051726","regulation of cell cycle",2.4136384028712428,-1.6965683256731625,-5.224386709038659,2.4313637641589874,-2.489126028656599,0.00324245510337673,0.9261987915405452,0.13318436),
  191. c("GO:0051781","positive regulation of cell division",0.3858232391206819,-1.4381982207414985,-2.4542090051247363,1.6434526764861874,-2.2511758244611624,0.00560820881292773,0.8935586893189175,0.34143052),
  192. c("GO:0061041","regulation of wound healing",0.21534320323014802,-4.596314113350494,-4.573367763758973,1.3979400086720377,-3.580596040061754,0.000262666060142401,0.9151598637584444,0.33111554),
  193. c("GO:0065007","biological regulation",48.31763122476447,-0.1683793796333545,1.3573623196059337,3.731266349075492,-3.2229080544998245,0.000598538299590222,1,-0),
  194. c("GO:0065008","regulation of biological quality",7.572902646926873,-0.7211161636019007,-5.061143912816906,2.926856708949692,-3.7067406854089664,0.000196453293736323,0.9264897878175581,0.14852762),
  195. c("GO:0065009","regulation of molecular function",0.6908927770300584,-4.366856771334694,-6.203605589352763,1.8920946026904804,-4.527480697736076,2.96837867043367E-05,0.9433703601571416,0.08087451),
  196. c("GO:0070072","vacuolar proton-transporting V-type ATPase complex assembly",0.03589053387169134,6.021198656491597,1.0027939216664532,0.6989700043360189,-2.3387461553871156,0.00458409748382216,0.953881920243343,0.37370505),
  197. c("GO:0070373","negative regulation of ERK1 and ERK2 cascade",0.1256168685509197,-3.2876306491139267,-3.705962521572224,1.1760912590556813,-2.2285298890742995,0.0059084030128338,0.8836634988155826,0.36228142),
  198. c("GO:0070633","transepithelial transport",0.053835800807537006,-5.721961248269752,0.9077433421003241,0.8450980400142568,-2.5991764319797968,0.00251665433012571,0.9728003774178844,0.19654123),
  199. c("GO:0071495","cellular response to endogenous stimulus",2.9161058770749215,5.783703141999477,-2.25690104192675,2.513217600067939,-3.214280045108886,0.000610548199557434,0.9491092313097711,0.22053456),
  200. c("GO:0071503","response to heparin",0.008972633467922835,4.354117797020033,-1.446154932224279,0.3010299956639812,-2.0892626638637988,0.00814211695040723,0.9638421947444861,0.30563231),
  201. c("GO:0071604","transforming growth factor beta production",0.026917900403768503,2.55000309250725,5.620440366127305,0.6020599913279624,-3.297047240241349,0.000504606406180089,0.8765803570431733,0.32423957),
  202. c("GO:0071696","ectodermal placode development",0.03589053387169134,6.1991640090952105,4.009918989527676,0.6989700043360189,-2.550871752405228,0.00281273131014059,0.8993221406101136,0.3253194),
  203. c("GO:0071698","olfactory placode development",0.01794526693584567,5.930676508627721,3.833891320011671,0.47712125471966244,-2.550871752405228,0.00281273131014059,0.899469644482505,0.30664938),
  204. c("GO:0071840","cellular component organization or biogenesis",20.834454912516822,2.1329062227629376,1.2839015073303364,3.3660492098002353,-2.625432305076031,0.00236901436914775,0.9885238898682858,0.0244052),
  205. c("GO:0071941","nitrogen cycle metabolic process",0.053835800807537006,-3.82610685185737,6.830159416483626,0.8450980400142568,-2.298677211261121,0.00502716093703814,0.975288733175941,0.10368085),
  206. c("GO:0072089","stem cell proliferation",0.19739793629430236,3.029422179039893,0.7439704141242988,1.3617278360175928,-2.665976397402888,0.00215786167924936,0.9829122966808371,0.01207275),
  207. c("GO:0072201","negative regulation of mesenchymal cell proliferation",0.026917900403768503,1.3973330278092506,-1.3262078146052505,0.6020599913279624,-3.6484311433447885,0.000224682297773467,0.9095460463177879,0.30406768),
  208. c("GO:0072497","mesenchymal stem cell differentiation",0.01794526693584567,5.788753239753051,4.923222214699111,0.47712125471966244,-2.0892626638637988,0.00814211695040723,0.8960373545259108,0.36341843),
  209. c("GO:0072521","purine-containing compound metabolic process",1.8932256617317182,-1.412498221591791,7.078463074998525,2.326335860928751,-2.8563637349110427,0.00139199047999832,0.9554802967042634,0.35415729),
  210. c("GO:0072593","reactive oxygen species metabolic process",0.2602063705697622,0.5040875355609125,7.046691750275784,1.4771212547196624,-9.046167971296773,8.99149751735013E-10,0.9550259515659969,0.2213876),
  211. c("GO:0080164","regulation of nitric oxide metabolic process",0.10767160161507401,3.909311095710675,-5.669464141379851,1.1139433523068367,-2.3531793093093913,0.00443425526842756,0.9236849154719063,0.22969538),
  212. c("GO:0090066","regulation of anatomical structure size",1.417676087931808,-3.910453955665597,-2.1826991471083588,2.2013971243204513,-3.0648120039603186,0.00086136653715164,0.9114800750383011,0.0876516),
  213. c("GO:0090130","tissue migration",0.2691790040376851,3.7420495140346928,5.027619162646729,1.4913616938342726,-2.89284697797623,0.0012798321687634,0.9109708704424766,0.33174804),
  214. c("GO:0097120","receptor localization to synapse",0.1525347689546882,-6.345347585954876,0.3232929441836715,1.255272505103306,-2.8771300184137694,0.00132699712389893,0.9698404131448163,0.20310791),
  215. c("GO:0097435","supramolecular fiber organization",1.5522655899506506,6.7112616926560245,0.8994490815544309,2.2405492482826,-2.879551624649551,0.00131961843914376,0.9502822880025517,0.29262693),
  216. c("GO:0098657","import into cell",1.857335127860027,-6.5757759262698645,1.1369237014770783,2.3180633349627615,-3.0907210026764114,0.000811482198841796,0.962721703559223,0.32373107),
  217. c("GO:0098696","regulation of neurotransmitter receptor localization to postsynaptic specialization membrane",0.008972633467922835,-3.9249483966701595,-1.5668200466351487,0.3010299956639812,-2.550871752405228,0.00281273131014059,0.9100518862966277,0.38815389),
  218. c("GO:0098727","maintenance of cell number",0.2691790040376851,5.815101514650029,4.294809899253818,1.4913616938342726,-2.083585227279172,0.00824925583670368,0.8910184492487822,0.36598448),
  219. c("GO:0098751","bone cell development",0.008972633467922835,4.992788505583942,4.942831047060622,0.3010299956639812,-2.1494934520550397,0.00708771992668034,0.8629990955452924,0.34779763),
  220. c("GO:0099003","vesicle-mediated transport in synapse",0.33198743831314487,-6.171842926375288,0.9176990915114892,1.5797835966168101,-4.486859745333333,3.25941946405701E-05,0.9597587427537869,0.22904897),
  221. c("GO:0104004","cellular response to environmental stimulus",0.7178106774338268,5.286013923665726,-2.3051066808056575,1.9084850188786497,-2.4681844272428406,0.0034026366284608,0.9607101171991778,0.22090751),
  222. c("GO:0120255","olefinic compound biosynthetic process",0.026917900403768503,2.4373464213699623,7.329507784122429,0.6020599913279624,-2.0003215805270225,0.00999259807549968,0.9614373684344166,0.22398541),
  223. c("GO:1900076","regulation of cellular response to insulin stimulus",0.1525347689546882,-4.441788752100383,-4.568237968012958,1.255272505103306,-2.167928619224323,0.00679315275911407,0.920474697615263,0.34253151),
  224. c("GO:1901184","regulation of ERBB signaling pathway",0.10767160161507401,-4.642698320036208,-3.9798347545688726,1.1139433523068367,-2.4896275119064404,0.00323871317583019,0.9166271375529436,0.35819543),
  225. c("GO:1901564","organonitrogen compound metabolic process",18.806639748766262,-0.9833771762426907,5.830996702297288,3.3215984304653436,-2.568510282088761,0.00270078316548836,0.9544656465098497,0.38090877),
  226. c("GO:1901615","organic hydroxy compound metabolic process",1.6778824585015704,-1.807771528545462,4.941334366007032,2.27415784926368,-3.6652614028563697,0.000216141717011251,0.9663910395302343,0.1495017),
  227. c("GO:1902027","positive regulation of cartilage condensation",0.008972633467922835,-1.5197868046036012,-1.52472847918408,0.3010299956639812,-2.0892626638637988,0.00814211695040723,0.9202394171794401,0.21578295),
  228. c("GO:1902047","polyamine transmembrane transport",0.008972633467922835,-6.053094260896948,2.428798034947273,0.3010299956639812,-2.345325514011268,0.00451517394522571,0.9677814354961719,0.17463091),
  229. c("GO:1902766","skeletal muscle satellite cell migration",0.01794526693584567,2.9348107164663464,-0.1901668594379421,0.47712125471966244,-3.3873653408434827,0.000409859172756446,0.982339392132666,0.00972304),
  230. c("GO:1903426","regulation of reactive oxygen species biosynthetic process",0.053835800807537006,4.257668738714352,-5.411466245860722,0.8450980400142568,-2.2564943108979376,0.00553994801024404,0.9208294024666634,0.21583204),
  231. c("GO:1904064","positive regulation of cation transmembrane transport",0.11664423508299686,-2.1628268208996047,-1.8821098822331712,1.146128035678238,-4.558478971987804,2.76389174021723E-05,0.8666389560984077,0.08143295),
  232. c("GO:1904407","positive regulation of nitric oxide metabolic process",0.06280843427545985,1.7701440937340076,-3.999436212005656,0.9030899869919435,-2.477893003502595,0.00332741520239066,0.8908513732316189,0.228564),
  233. c("GO:1904888","cranial skeletal system development",0.19739793629430236,5.697882399344226,4.084907256587084,1.3617278360175928,-2.0251329573681267,0.00943771900388291,0.8859391868840478,0.38261162),
  234. c("GO:1990535","neuron projection maintenance",0.03589053387169134,7.403471629041254,-0.09985788651286498,0.6989700043360189,-2.916159785640011,0.00121294250251457,0.9534745960839488,0.19975571),
  235. c("GO:1990845","adaptive thermogenesis",0.07178106774338268,-2.794415707200205,3.7211361982371063,0.9542425094393249,-2.1231165368362723,0.00753153438448695,0.9747346262205613,0.10640877),
  236. c("GO:2000241","regulation of reproductive process",0.4037685060565276,0.03604132819391131,-0.4420550835572254,1.662757831681574,-2.03473209672883,0.00923140709432059,0.9422496930765117,0.08249675),
  237. c("GO:2000243","positive regulation of reproductive process",0.23328847016599372,-1.4663282538627935,-2.059786445093361,1.4313637641589874,-2.642374162075567,0.00227837831210199,0.9020474590310131,0.25196873),
  238. c("GO:2000628","regulation of miRNA metabolic process",0.22431583669807087,3.406550006997988,-5.870164410743355,1.414973347970818,-2.250436912145785,0.00561775878887449,0.9140088926438991,0.27774149),
  239. c("GO:2000772","regulation of cellular senescence",0.09869896814715118,3.7991027250694125,-5.207630077539204,1.0791812460476249,-2.045261046717194,0.00901029382007512,0.9196499726480126,0.22785813),
  240. c("GO:2000773","negative regulation of cellular senescence",0.06280843427545985,2.50606035826854,-3.925550667813852,0.9030899869919435,-2.345325514011268,0.00451517394522571,0.8915468861729953,0.32609844),
  241. c("GO:2001057","reactive nitrogen species metabolic process",0.08075370121130553,-1.4131966546554249,2.9159819454860787,1,-2.2564943108979376,0.00553994801024404,0.9745003135107876,0.1075675))
  243. one.data <- data.frame(revigo.data)
  244. names(one.data) <- revigo.names
  246. one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ]
  247. one.data$plot_X <- as.numeric( as.character(one.data$plot_X) )
  248. one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) )
  249. one.data$log_size <- as.numeric( as.character(one.data$log_size) )
  250. one.data$value <- as.numeric( as.character(one.data$value) )
  251. one.data$frequency <- as.numeric( as.character(one.data$frequency) )
  252. one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) )
  253. one.data$dispensability <- as.numeric( as.character(one.data$dispensability) )
  254. #head(one.data);
  256. terms <- read.csv("tables/Supp_table_3.csv") %>%
  257. filter(sample == "Devel") %>%
  258. filter(P.DE < 0.05)
  260. term_color <- terms[, c("ID", "module")] %>%
  261. mutate(module = str_remove(module, "^\\d+_")) %>%
  262. rename("term_ID" = "ID")
  264. module_order <- c("magenta","pink","lightyellow","red","black","green","greenyellow",
  265. "grey60","tan","yellow","salmon","darkgreen","royalblue","blue",
  266. "lightcyan","purple","midnightblue","cyan","brown","turquoise","lightgreen","darkred")
  268. one.data <- left_join(one.data, term_color, by = "term_ID") %>%
  269. dplyr::arrange(dispensability) %>%
  270. mutate(module = factor(module, levels = module_order))
  272. ex <- one.data [ one.data$dispensability < 0.15, ];
  273. one.x_range = max(one.data$plot_X) - min(one.data$plot_X);
  274. one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);
  276. p1 <- ggplot(data = one.data,
  277. aes(x = plot_X,
  278. y = plot_Y,
  279. color = module,
  280. size = -value,
  281. label = description)) +
  282. geom_point(pch = 21) +
  283. scale_color_manual(values = module_order) +
  284. scale_size( range=c(2, 16)) +
  285. theme_bw() +
  286. labs (x = "semantic space x", y = "semantic space y") +
  287. theme(legend.key = element_blank()) +
  288. xlim(min(one.data$plot_X)-one.x_range/200,max(one.data$plot_X)+one.x_range/200) +
  289. ylim(min(one.data$plot_Y)-one.y_range/200,max(one.data$plot_Y)+one.y_range/200);
  291. plotly::ggplotly(p1)
  294. pdf("figures/Supp_Fig_2_revigo_semantic_space_galgal.pdf", paper = "a4", height = 8, width = 8)
  295. p1 + geom_point() +
  296. theme(legend.position = "none")
  297. dev.off()
  299. # Facet by module
  301. facet <- ggplot(data = one.data[,c(2,4,5,7)],
  302. aes(x = plot_X,
  303. y = plot_Y,
  304. size = -value,
  305. label = description)) +
  306. geom_point(color= "grey90") +
  307. geom_point(data = one.data,
  308. aes(x = plot_X,
  309. y = plot_Y,
  310. size = -value,
  311. fill = module),
  312. pch = 21,
  313. color = "black") +
  314. scale_fill_manual(values = module_order) +
  315. scale_size( range=c(0.5, 8)) +
  316. theme_classic() +
  317. labs (x = "semantic space x", y = "semantic space y") +
  318. theme(legend.key = element_blank()) +
  319. xlim(min(one.data$plot_X)-one.x_range/200,max(one.data$plot_X)+one.x_range/200) +
  320. ylim(min(one.data$plot_Y)-one.y_range/200,max(one.data$plot_Y)+one.y_range/200) +
  321. facet_wrap(vars(module), nrow = 4, ncol = 6) +
  322. theme(legend.position = "none")
  324. pdf("figures/Fig_2_revigo_semantic_space_galgal_facet.pdf", height = 8, width = 10)
  325. facet
  326. dev.off()

REVIGO_Gg_devel_modules.R at commit 2e4f440, no license · at the source

Overview

Authors: Fabio Sacher1, Bianka Berki1, Antoine Fages1, Libby Gavrilov2, Avihu Klar2, Maëva Luxey1, Patrick Tschopp1
ORCID iDs: Fabio Sacher, Patrick Tschopp
  1. DUW Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
  2. Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
Institutions: University of Basel (Switzerland); Hebrew University of Jerusalem (Israel); Hadassah Medical Center (Israel)
Journal: iScience, volume 29, issue 4, article 115196
Dates: received 3 June 2025; accepted 26 February 2026; published online 3 March 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1016/j.isci.2026.115196 · PMID 41884005 · PMCID PMC13010115 · OpenAlex W7133317416
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: other (organism)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Spectral & time-frequency, Connectivity
Keywords: Molecular biology, Neuroscience, Developmental biology, Omics
Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex
Funding: Olga Mayenfisch Foundation; Swiss National Science Foundation (310030, 170022); United States - Israel Binational Science Foundation; Schweizerische Stiftung für die Erforschung der Muskelkrankheiten; Janggen-Pöhn Foundation
Citations: cited by 1 paper (Europe PMC); 122 references in the paper
Research resources: Anti-Digoxigenin-AP RRID:AB_2734716, Foxp1 RRID:AB_732428

Abstract

The chicken spinal cord is a classic model system to study the early specification of neuronal cell types along its anterior-posterior axis. Here, we follow the ensuing maturation dynamics at limb levels with single-cell resolution and contrast neuronal populations innervating appendages of distinct form and function. We use gene co-expression modules to identify rare cell populations with specific biological functions, and show that appendages with different motor outputs – wings and legs – rely on largely similar spinal cord cell type repertoires. Challenging the system with experimental alterations to the peripheral limb musculature reveals limited transcriptional changes, but spatially restricted plasticity in spinal cord motor neuron numbers. Collectively, our results provide a resource to investigate the molecular and cellular basis of neuronal maturation in the avian spinal cord and highlight the plastic nature of embryonic cells to adapt to changes in the limb periphery at both developmental and evolutionary timescales.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 15 matches between paragraphs and lines of code.

safabio/spinal_cord_paper

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 2e4f440052cd4865cc4c4cd5ee81f31f327a49e6, 25 November 2025
Languages: R (62), Shell (20)
Size: 340 files, 82 scripts
Software Heritage: not archived
Found in: “Data and code availability”
Holds: README, 51 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Seurat (56 files), tidyverse (55 files), ggplot2 (50 files), patchwork (38 files), cowplot (33 files), pheatmap (10 files), limma (5 files), SingleCellExperiment (3 files), Plotly (2 files), DESeq2 (1 file), ggpubr (1 file), reshape2 (1 file), WGCNA (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
83 files
At the source: github.com/safabio/spinal_cord_paper

Zenodo 18553805

License: CC-BY-4.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data and code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
At the source: doi.org/10.5281/zenodo.18553805

CFeregrino/scWGCNA

License: GPL-3.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 316f28d60018fb5c7cc75435ca3be01ac4d8bb5a, 8 November 2022
Languages: R (12)
Size: 52 files, 12 scripts
Software Heritage: not archived
Found in: the resources table
Holds: README, license file, environment (DESCRIPTION), documentation, 1 notebook
Not found: CITATION.cff, tests, continuous integration
Tools: WGCNA (8 files), Seurat (6 files), reshape2 (2 files), ggplot2 (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
14 files
At the source: github.com/CFeregrino/scWGCNA

marionilab/milor

License: GPL-3.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 4ecad8927609d906520f36c54cb24f96e79655ee, 19 August 2026
Languages: R (53), C++ (10), JavaScript (7), C/C++ (7)
Size: 187 files, 77 scripts
Software Heritage: archived
Found in: the resources table
Holds: README, license file, environment (DESCRIPTION), tests, continuous integration, documentation, 4 notebooks
Not found: CITATION.cff
Tools: SingleCellExperiment (25 files), igraph (10 files), patchwork (6 files), tidyverse (6 files), edgeR (2 files), ggplot2 (2 files), limma (2 files), cowplot (1 file), Seurat (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
79 files
At the source: github.com/MarioniLab/miloR?tab=readme-ov-file

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 4 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 171 scripts, each with its path and the digest of its content;
  • 15 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data and code availability

Data: Raw data and processed count tables are publicly available on the Gene Expression Omnibus (GEO) under accession number GEO: GSE297980 (https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE297980).

Code: All original code is publicly available on GitHub under https://github.com/safabio/spinal_cord_paper (https://doi.org/10.5281/zenodo.18553805).

Additional information: Any additional information required to reanalyze the data reported in this article will be shared by the lead contact upon request.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 4 keywords, 5 funders, 119 references, 2 RRIDs.

Cite

This paper

Sacher, F., Berki, B., Fages, A., Gavrilov, L., Klar, A., Luxey, M., & Tschopp, P. (2026). Transcriptional and cellular maturation of the chick spinal cord in the context of distinct neuromuscular circuits. iScience, 29(4), 115196. https://doi.org/10.1016/j.isci.2026.115196

BibTeX

@article{sacher2026transcriptional,
author = {Sacher, Fabio and Berki, Bianka and Fages, Antoine and Gavrilov, Libby and Klar, Avihu and Luxey, Maëva and Tschopp, Patrick},
title = {{Transcriptional and cellular maturation of the chick spinal cord in the context of distinct neuromuscular circuits}},
journal = {iScience},
year = {2026},
month = mar,
volume = {29},
number = {4},
pages = {115196},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.115196},
url = {https://doi.org/10.1016/j.isci.2026.115196},
pmid = {41884005},
pmcid = {PMC13010115}
}

RIS

TY - JOUR
AU - Sacher, Fabio
AU - Berki, Bianka
AU - Fages, Antoine
AU - Gavrilov, Libby
AU - Klar, Avihu
AU - Luxey, Maëva
AU - Tschopp, Patrick
TI - Transcriptional and cellular maturation of the chick spinal cord in the context of distinct neuromuscular circuits
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/03/03
VL - 29
IS - 4
SP - 115196
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.115196
UR - https://doi.org/10.1016/j.isci.2026.115196
LA - en
ER -

CSL-JSON

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"container-title": "iScience",
"author": [
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"family": "Sacher",
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{
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{
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{
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},
{
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"given": "Patrick"
}
],
"container-title-short": "iScience",
"volume": "29",
"issue": "4",
"page": "115196",
"DOI": "10.1016/j.isci.2026.115196",
"PMID": "41884005",
"PMCID": "PMC13010115",
"ISSN": "2589-0042",
"publisher": "Elsevier",
"URL": "https://doi.org/10.1016/j.isci.2026.115196",
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
3
]
]
}
}

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