OSCR

<i>HMGA2</i> regulates fear and growth: Canine GWAS and functional evidence.

Code ↔ Paper

2 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 2 matches
  1. [1] § STAR★Methods › Method details › Genome wide association analysis ↔ src/gemma_io.h, lines 1–60 · score 0.56 · mixed models, genome wide, Gemma
  2. [2] § STAR★Methods › Method details › Genome wide association analysis ↔ src/debug.h, lines 1–84 · score 0.56 · mixed models, genome wide, Gemma, matrix

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

C/C++ header · 187 lines · 9.2 KB · GPL-3.0 · 1 match

  1. /*
  2. Genome-wide Efficient Mixed Model Association (GEMMA)
  3. Copyright © 2011-2017, Xiang Zhou
  4. Copyright © 2017, Peter Carbonetto
  5. Copyright © 2017, Pjotr Prins
  7. This program is free software: you can redistribute it and/or modify
  8. it under the terms of the GNU General Public License as published by
  9. the Free Software Foundation, either version 3 of the License, or
  10. (at your option) any later version.
  12. This program is distributed in the hope that it will be useful,
  13. but WITHOUT ANY WARRANTY; without even the implied warranty of
  14. MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  15. GNU General Public License for more details.
  17. You should have received a copy of the GNU General Public License
  18. along with this program. If not, see <http://www.gnu.org/licenses/>.
  19. */
  21. #ifndef __IO_H__
  22. #define __IO_H__
  24. #include "gsl/gsl_matrix.h"
  25. #include "gsl/gsl_vector.h"
  26. #include <algorithm>
  27. #include <map>
  28. #include <vector>
  30. #include "gzstream.h"
  31. #include "param.h"
  33. #define tab(col) ( col ? "\t" : "")
  35. using namespace std;
  37. void ProgressBar(string str, double p, double total, double ratio = -1.0);
  39. std::istream &safeGetline(std::istream &is, std::string &t);
  41. bool ReadFile_snps(const string file_snps, set<string> &setSnps);
  42. bool ReadFile_snps_header(const string &file_snps, set<string> &setSnps);
  43. bool ReadFile_log(const string &file_log, double &pheno_mean);
  45. bool ReadFile_bim(const string &file_bim, vector<SNPINFO> &snpInfo);
  46. bool ReadFile_fam(const string &file_fam, vector<vector<int>> &indicator_pheno,
  47. vector<vector<double>> &pheno, map<string, int> &mapID2num,
  48. const vector<size_t> &p_column);
  50. bool ReadFile_cvt(const string &file_cvt, vector<int> &indicator_cvt,
  51. vector<vector<double>> &cvt, size_t &n_cvt);
  52. bool ReadFile_anno(const string &file_bim, map<string, string> &mapRS2chr,
  53. map<string, long int> &mapRS2bp,
  54. map<string, double> &mapRS2cM);
  55. bool ReadFile_pheno(const string &file_pheno,
  56. vector<vector<int>> &indicator_pheno,
  57. vector<vector<double>> &pheno,
  58. const vector<size_t> &p_column);
  59. bool ReadFile_column(const string &file_pheno, vector<int> &indicator_idv,
  60. vector<double> &pheno, const int &p_column);
  62. bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
  63. const gsl_matrix *W, vector<int> &indicator_idv,
  64. vector<int> &indicator_snp, const double &maf_level,
  65. const double &miss_level, const double &hwe_level,
  66. const double &r2_level, map<string, string> &mapRS2chr,
  67. map<string, long int> &mapRS2bp,
  68. map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
  69. size_t &ns_test);
  70. bool ReadFile_bed(const string &file_bed, const set<string> &setSnps,
  71. const gsl_matrix *W, vector<int> &indicator_idv,
  72. vector<int> &indicator_snp, vector<SNPINFO> &snpInfo,
  73. const double &maf_level, const double &miss_level,
  74. const double &hwe_level, const double &r2_level,
  75. size_t &ns_test);
  76. bool Bimbam_ReadOneSNP(const size_t inc, const vector<int> &indicator_idv,
  77. igzstream &infile, gsl_vector *geno, double &geno_mean);
  78. void Plink_ReadOneSNP(const int pos, const vector<int> &indicator_idv,
  79. ifstream &infile, gsl_vector *geno, double &geno_mean);
  81. void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
  82. map<string, int> &mapID2num, const size_t k_mode, bool &error,
  83. gsl_matrix *G);
  84. void ReadFile_mk(const string &file_mk, vector<int> &indicator_idv,
  85. map<string, int> &mapID2num, const size_t k_mode, bool &error,
  86. gsl_matrix *G);
  87. void ReadFile_eigenU(const string &file_u, bool &error, gsl_matrix *U);
  88. void ReadFile_eigenD(const string &file_d, bool &error, gsl_vector *eval);
  90. bool BimbamKin(const string file_geno, const set<string> ksnps,
  91. vector<int> &indicator_snp, const int k_mode,
  92. const int display_pace, gsl_matrix *matrix_kin,
  93. const bool test_nind);
  94. bool PlinkKin(const string &file_bed, vector<int> &indicator_snp,
  95. const int k_mode, const int display_pace, gsl_matrix *matrix_kin);
  97. bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv,
  98. vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K,
  99. const bool calc_K);
  100. bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv,
  101. vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K,
  102. const bool calc_K);
  103. bool ReadFile_geno(const string &file_geno, vector<int> &indicator_idv,
  104. vector<int> &indicator_snp,
  105. vector<vector<unsigned char>> &Xt, gsl_matrix *K,
  106. const bool calc_K, const size_t ni_test,
  107. const size_t ns_test);
  108. bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv,
  109. vector<int> &indicator_snp, vector<vector<unsigned char>> &Xt,
  110. gsl_matrix *K, const bool calc_K, const size_t ni_test,
  111. const size_t ns_test);
  113. bool ReadFile_est(const string &file_est, const vector<size_t> &est_column,
  114. map<string, double> &mapRS2est);
  116. bool CountFileLines(const string &file_input, size_t &n_lines);
  118. bool ReadFile_gene(const string &file_gene, vector<double> &vec_read,
  119. vector<SNPINFO> &snpInfo, size_t &ng_total);
  121. bool ReadHeader_io(const string &line, HEADER &header);
  122. bool ReadFile_cat(const string &file_cat, map<string, size_t> &mapRS2cat,
  123. size_t &n_vc);
  124. bool ReadFile_mcat(const string &file_mcat, map<string, size_t> &mapRS2cat,
  125. size_t &n_vc);
  127. bool ReadFile_catc(const string &file_cat,
  128. map<string, vector<double>> &mapRS2catc, size_t &n_cat);
  129. bool ReadFile_mcatc(const string &file_mcat,
  130. map<string, vector<double>> &mapRS2catc, size_t &n_cat);
  132. bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
  133. const int display_pace,
  134. const vector<int> &indicator_idv,
  135. const vector<int> &indicator_snp,
  136. const map<string, double> &mapRS2weight,
  137. const map<string, size_t> &mapRS2cat,
  138. const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
  139. gsl_matrix *matrix_kin, gsl_vector *vector_ns);
  140. bool PlinkKin(const string &file_bed, const int display_pace,
  141. const vector<int> &indicator_idv,
  142. const vector<int> &indicator_snp,
  143. const map<string, double> &mapRS2weight,
  144. const map<string, size_t> &mapRS2cat,
  145. const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
  146. gsl_matrix *matrix_kin, gsl_vector *vector_ns);
  147. bool MFILEKin(const size_t mfile_mode, const string &file_mfile,
  148. const set<string> setKSnps, const int display_pace,
  149. const vector<int> &indicator_idv,
  150. const vector<vector<int>> &mindicator_snp,
  151. const map<string, double> &mapRS2weight,
  152. const map<string, size_t> &mapRS2cat,
  153. const vector<vector<SNPINFO>> &msnpInfo, const gsl_matrix *W,
  154. gsl_matrix *matrix_kin, gsl_vector *vector_ns);
  156. bool ReadFile_wsnp(const string &file_wsnp, map<string, double> &mapRS2double);
  157. bool ReadFile_wsnp(const string &file_wcat, const size_t n_vc,
  158. map<string, vector<double>> &mapRS2vector);
  160. void ReadFile_beta(const string &file_beta,
  161. const map<string, size_t> &mapRS2cat,
  162. const map<string, double> &mapRS2wA, vector<size_t> &vec_cat,
  163. vector<size_t> &vec_ni, vector<double> &vec_weight,
  164. vector<double> &vec_z2, size_t &ni_total, size_t &ns_total,
  165. size_t &ns_test);
  166. void ReadFile_beta(const string &file_beta, const map<string, double> &mapRS2wA,
  167. map<string, string> &mapRS2A1, map<string, double> &mapRS2z);
  168. void Calcq(const size_t n_block, const vector<size_t> &vec_cat,
  169. const vector<size_t> &vec_ni, const vector<double> &vec_weight,
  170. const vector<double> &vec_z2, gsl_matrix *Vq, gsl_vector *q,
  171. gsl_vector *s);
  173. void ReadFile_study(const string &file_study, gsl_matrix *Vq, gsl_vector *q_vec,
  174. gsl_vector *s_vec, size_t &ni);
  175. void ReadFile_ref(const string &file_ref, gsl_matrix *S_mat,
  176. gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
  177. void ReadFile_mstudy(const string &file_mstudy, gsl_matrix *Vq,
  178. gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni);
  179. void ReadFile_mref(const string &file_mref, gsl_matrix *S_mat,
  180. gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
  181. bool ReadFile_sample(const string &file_sample,
  182. vector<vector<int>> &indicator_pheno,
  183. vector<vector<double>> &pheno,
  184. const vector<size_t> &p_column, vector<int> &indicator_cvt,
  185. vector<vector<double>> &cvt, size_t &n_cvt);
  187. #endif

gemma_io.h at commit ce5e778, under GPL-3.0 · at the source

Overview

Authors: Yun Yu1, Chao Li1,2, Ye Liu1,2, Yinyu Su3, Xuebin Wang1, James A. Serpell4, Shurun Zhang1, Jinxue Ruan3, Yanhu Liu1,5, Ya-Ping Zhang1,2,5,6
ORCID iDs: Yun Yu, Ya-Ping Zhang
  1. State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
  2. State Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
  3. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P.R. China
  4. School of Veterinary Medicine, University of Pennsylvania, 3900 Delancey Street, Philadelphia, PA 19104, USA
  5. KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
  6. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
Institutions: Kunming Institute of Zoology (China); Chinese Academy of Sciences (China); Yunnan University (China); Huazhong Agricultural University (China); University of Pennsylvania (United States); University of Chinese Academy of Sciences (China)
Journal: iScience, volume 29, issue 7, article 116429
Dates: received 13 January 2026; accepted 1 June 2026; published online 17 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.isci.2026.116429 · PMID 42369036 · PMCID PMC13293657 · OpenAlex W7165029143
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), mouse (organism), other (organism)
Methods: Spectral & time-frequency, Statistics
Keywords: canine behavior, genomics, behavioral neuroscience
Topic: Human-Animal Interaction Studies (Genetics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: STI2030-Major Projects (2021ZD0203900); National Natural Science Foundation of China (National Science Foundation of China) (32302737); National Key Research and Development Program of China (2019YFA0707101); Spring City·Plan: the High-level Talent Promotion and Training Project of Kunming (2022SCP001); Key Research and Development Program of Yunnan Province (202203AC100010); Key Research Program of Frontier Sciences of the Chinese Academy of Sciences (CAS) (ZDBS-LY-SM011); Project of Qingdao Emerging Industry Cultivation Plan (23-1-4-xxgg-21-nsh); Shandong Province Small and Medium-Sized High-Tech Enterprise Innovation Capacity Enhancement Project (2023TSGC0506); Yunnan Fundamental Research Projects (202401CF070061)
Citations: not cited yet (Europe PMC); 75 references in the paper
Research resources: HMGA2 antibody RRID:AB_10679322, anti-rabbit RRID:AB_2099233, β-actin antibody RRID:AB_2737399, anti-mouse RRID:AB_330924, The MDCK cell line RRID:CVCL_0422, catalog number CRL-11268 RRID:CVCL_1926

Abstract

Fear is an evolutionarily conserved survival mechanism. Fear behavior is strongly correlated with body size in dogs, the genetic basis of fear regulation independent of size-related traits remains unclear. Through cross-breed genome-wide association analysis, we identified association between HMGA2 gene and fear traits. Our functional validation revealed that viral overexpression of Hmga2 in the mouse basolateral amygdala attenuated fear memory formation independent of body weight, while Hmga2 knockout (KO) mice exhibited enhanced fear memory. Transcriptomic analyses linked Hmga2 to modulation of neurotransmitter activity, synaptic plasticity (including GABAergic signaling), and neurogenesis, with additional roles in early brain development revealed by embryonic KO studies. We also identified a mutation in an enhancer that can regulate HMGA2 expression in human HEK293T cell line. Our findings establish HMGA2 as a pleiotropic regulator of fear behavior decoupled from its effects on body size, resolving a long-standing confound in canine behavioral genetics.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

genetics-statistics/GEMMA

License: GPL-3.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: ce5e778cc36c40a2fa82f3dafe66403bb0e3a185, 10 December 2025
Languages: C++ (21), C/C++ (21), Shell (5), Perl (1)
Size: 141 files, 48 scripts
Software Heritage: not archived
Found in: the text, “Key resources table”
Holds: README, license file, tests, continuous integration, documentation
Not found: CITATION.cff, environment file
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
50 files
At the source: github.com/genetics-statistics/GEMMA

deweylab/RSEM

License: GPL-3.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 800234e0d25d16bf7042804604c4371f12b96d9e, 3 August 2026
Languages: C/C++ (180), C (111), C++ (48), Perl (16), Python (11), R (11), Shell (7), Java (1)
Size: 3,057 files, 385 scripts
Software Heritage: not archived
Found in: the text, “Key resources table”
Holds: README, license file, environment (tests/environment.yml, pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/DESCRIPTION, pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/DESCRIPTION), tests, continuous integration, documentation
Not found: CITATION.cff
Tools: data.table (2 files), STAR (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
387 files
At the source: github.com/deweylab/RSEM

OpenGene/fastp

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 8a2397b6628ae14127efdb7566f67fc05f9aea56, 10 September 2026
Languages: C/C++ (34), C++ (29), Shell (2), Python (1)
Size: 73 files, 66 scripts
Software Heritage: not archived
Found in: the text, “Key resources table”
Holds: README, license file, continuous integration
Not found: CITATION.cff, environment file, tests, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
68 files
At the source: github.com/OpenGene/fastp

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:

  • 3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 499 scripts, each with its path and the digest of its content;
  • 2 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

• Variant file in vcf format from the Dog10K project was collected from website https://kiddlabshare.med.umich.edu/dog10K/. RNA-seq data have been deposited at Genome Sequence Archive (GSA) as CRA016531 and are publicly available as of the date of publication. • Original western blot images have been deposited at Mendeley at (https://doi.org/10.17632/b27xm6wcr6.1) and are publicly available as of the date of publication. Microscopy data reported in this paper will be shared by the lead contact upon request. • This paper does not report original code. • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. The C-BARQ data reported in this study cannot be deposited in a public repository because of copyright restrictions. C-BARQ behavior data were provided by James Serpell. To request access, contact James A. Serpell for requesting access.

Reproduced under the paper's license (CC BY), 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 2, 28 September 2026

  • Authors: added Ya-Ping Zhang (0000-0002-5401-1114); removed Ya-Ping Zhang

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 3 keywords, 9 funders, 73 references, 6 RRIDs.

Cite

This paper

Yu, Y., Li, C., Liu, Y., Su, Y., Wang, X., Serpell, J. A., Zhang, S., Ruan, J., Liu, Y., & Zhang, Y.-P. (2026). &lt;i&gt;HMGA2&lt;/i&gt; regulates fear and growth: Canine GWAS and functional evidence. iScience, 29(7), 116429. https://doi.org/10.1016/j.isci.2026.116429

BibTeX

@article{yu2026lt,
author = {Yu, Yun and Li, Chao and Liu, Ye and Su, Yinyu and Wang, Xuebin and Serpell, James A. and Zhang, Shurun and Ruan, Jinxue and Liu, Yanhu and Zhang, Ya-Ping},
title = {{\&lt;i\&gt;HMGA2\&lt;/i\&gt; regulates fear and growth: Canine GWAS and functional evidence}},
journal = {iScience},
year = {2026},
month = jun,
volume = {29},
number = {7},
pages = {116429},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.116429},
url = {https://doi.org/10.1016/j.isci.2026.116429},
pmid = {42369036},
pmcid = {PMC13293657}
}

RIS

TY - JOUR
AU - Yu, Yun
AU - Li, Chao
AU - Liu, Ye
AU - Su, Yinyu
AU - Wang, Xuebin
AU - Serpell, James A.
AU - Zhang, Shurun
AU - Ruan, Jinxue
AU - Liu, Yanhu
AU - Zhang, Ya-Ping
TI - &lt;i&gt;HMGA2&lt;/i&gt; regulates fear and growth: Canine GWAS and functional evidence
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/06/17
VL - 29
IS - 7
SP - 116429
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.116429
UR - https://doi.org/10.1016/j.isci.2026.116429
LA - en
ER -

CSL-JSON

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"container-title": "iScience",
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CRISPR-engineered deletion of POGZ alters transcription factor binding at promoters of genes involved in synaptic signaling.
Journal: HGG advances
In common: STAR, data.table, 3 references

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