Personalized functional topography-based multisite brain age prediction modeling reveals divergent neurodevelopment in major depression.
The 2 matches
- [1] § Materials and Methods › Examining the Associations between Gene Expression and BAG-Related Functional Topography. ↔ 4.gene/s1_brainspan.m, lines 28–98 · score 0.57 · neurodevelopmental processes, axon, synapse, dendrite, BrainSpan, genes
- [2] § Materials and Methods › Calculating Individualized Functional Network Topography. ↔ 1.Predict_brain_age/s1.NMF/src/backNMF_u.m, lines 1–70 · score 0.55 · fMRI, spatial maps, NMF, matrix, age
Paper
Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC
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The authors' code
MATLAB · 98 lines · 4.5 KB · no license · 1 match
- load('D:\study\sub2\brain_age\brain_span\age_cortical_am_hip.mat','age_new_day')
- load('D:\study\sub2\brain_age\brain_span\column_pos_cortical_am_hip.mat','column_pos')
- data = readmatrix('D:\study\sub2\brain_age\brain_span\expression_matrix_my.csv');
- data_new=data(:,column_pos);
- filename = 'D:\study\sub2\brain_age\brain_span\columns_metadata.csv';
- opts = detectImportOptions(filename);
- opts.SelectedVariableNames = opts.VariableNames(7);
- strData = readmatrix(filename, opts, 'OutputType', 'string');
- brain_new=strData(column_pos);
- rowsToDelete = all(data_new == 0, 2);
- data_new(rowsToDelete, :) = [];
- filename = 'D:\study\sub2\brain_age\brain_span\rows_metadata.csv';
- opts = detectImportOptions(filename);
- opts.SelectedVariableNames = opts.VariableNames(4); % 选择第一列
- strData = readmatrix(filename, opts, 'OutputType', 'string');
- gene_new=strData;
- gene_new(rowsToDelete)=[];
- %%
- condi='sub1'
- domi_pos=find(brain_new=='OFC'|brain_new=='ITC'|brain_new=='STC');
- domi_notpos=find(~(brain_new=='OFC'|brain_new=='ITC'|brain_new=='STC'));
- %condi='sub2'
- %domi_pos=find(brain_new=='M1C'|brain_new=='V1C'|brain_new=='VFC'|brain_new=='HIP'|brain_new=='AMY'|brain_new=='DFC');
- %domi_notpos=find(~(brain_new=='M1C'|brain_new=='V1C'|brain_new=='VFC'|brain_new=='HIP'|brain_new=='AMY'|brain_new=='DFC'));
- %%
- load('D:\study\sub2\brain_age\brain_span\neurodev_proc.mat');
- field = fieldnames(neurodev_proc); % four neurodevelopment processes
- for i = 1:length(field)
- i
- proc = field{i};
- gene_proc = getfield(neurodev_proc, proc);
- [isMember, indexInB] = ismember(gene_new, gene_proc);
- genepos1 = find(isMember);
- gene_remain_pos=find(isMember==0);
- gene_domi1=data_new(genepos1,domi_pos);
- gene_nodomi1=data_new(genepos1,domi_notpos);
- Data = zscore( [ gene_domi1'; gene_nodomi1' ] );%region(domi/nodomi)*gene(developmental process gene)
- [ ~, PC ] = pca( Data, 'Centered', false );
- if corr( PC( :, 1 ), mean( Data, 2 ) ) < 0
- PC = -PC;
- end
- PC = PC(:,1);%region*1
- PC_normalized = (PC- min(PC)) ./ (max(PC) - min(PC));
- % for trajactory
- domAge = log2(age_new_day(domi_pos));%是domi 脑区的那些年龄
- notdomAge = log2(age_new_day(domi_notpos));%不是domi 脑区的那些年龄
- domPC_minmax = PC_normalized(1:size(gene_domi1,2));% Data = zscore( [ gene_domi1'; gene_nodomi1' ] );%region*gene
- notdomPC_minmax = PC_normalized((size(gene_domi1,2)+1):end);
- dataTable = table(domAge, domPC_minmax, 'VariableNames', {'age', 'y'});
- filename = strcat('D:\study\sub2\brain_age\brain_span\',proc,'_',condi,'_domi_cortical.xlsx');
- writetable(dataTable, filename);
- dataTable = table(notdomAge, notdomPC_minmax, 'VariableNames', {'age', 'y'});
- filename = strcat('D:\study\sub2\brain_age\brain_span\',proc,'_',condi,'_nodomi_cortical.xlsx');
- writetable(dataTable, filename);
- % for significant analyze
- domPC = PC(1:length(domAge));
- notdomPC = PC((length(domAge)+1):end);
- Index_dom_6_14 = find(domAge >= log2(4281) & domAge <= log2(14866));
- Index_notdom_6_14 = find(notdomAge >=log2(4281) & notdomAge <=log2(14866));%here
- domPC_6_14 = mean(domPC(Index_dom_6_14));
- notdomPC_6_14 = mean(notdomPC(Index_notdom_6_14));
- diff_PC(i) = domPC_6_14 - notdomPC_6_14;
- nperm = 1000; % permutation number
- for j = 1 : nperm
- j
- myresample = randsample(length(gene_remain_pos),length(genepos1));
- myresample=gene_remain_pos(myresample);
- domGene_perm = data_new(myresample,domi_pos);
- notdomGene_perm = data_new(myresample,domi_notpos);
- Dataperm = zscore( [ domGene_perm'; notdomGene_perm' ] );
- [ ~, PCperm ] = pca( Dataperm, 'Centered', false );
- if corr( PCperm( :, 1 ), mean( Dataperm, 2 ) ) < 0
- PCperm = -PCperm;
- end
- domPCperm = PCperm(1:length(domAge));
- notdomPCperm = PCperm((length(domAge) + 1):end);
- domPCperm_6_14 = mean(domPCperm(Index_dom_6_14));
- notdomPCperm_6_14 = mean(notdomPCperm(Index_notdom_6_14));
- diff_PCperm(j,i) = domPCperm_6_14 - notdomPCperm_6_14;
- end
- if diff_PC(i) > 0
- p_perm(i) = length(find(diff_PCperm(:,i) > diff_PC(i))) / nperm;
- else
- p_perm(i) = length(find(diff_PCperm(:,i) < diff_PC(i))) / nperm;
- end
- end
- Myelin=diff_PCperm(:,1);
- Axon=diff_PCperm(:,2);
- Dendrite=diff_PCperm(:,3);
- Synapse=diff_PCperm(:,6);
- %save('D:\study\sub2\draw\permut_all.mat','Myelin','Axon','Dendrite','Synapse')
- % save('D:\study\sub2\draw\permut_sub1_cortical.mat','Myelin','Axon','Dendrite','Synapse')
- save('D:\study\sub2\draw\permut_sub1.mat','Myelin','Axon','Dendrite','Synapse')
s1_brainspan.m at commit ce1c5e7, no license · at the source
Overview
and 13 other authors
Qiyong Gong17,18,19, Tianmei Si16, Shijun Qiu15, Ching-Po Lin22,23,24, Jingliang Cheng13, Yanqing Tang25, Fei Wang25, Jiang Qiu11,12, Peng Xie26,27, Lingjiang Li5,6, Yong He1,2,3,28, DIDA-MDD Working Group, Mingrui Xia1,2,328 affiliations
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing 100875, China
- International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
- School of Systems Science, Beijing Normal University, Beijing 100875, China
- Department of Psychiatry and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
- Mental Health Institute of Central South University, China National Technology Institute on Mental Disorders, Hunan Technology Institute of Psychiatry, Hunan Key Laboratory of Psychiatry and Mental Health, Hunan Medical Center for Mental Health, National Technology Institute on Mental Disorders, Hunan Technology Institute of Psychiatry, Changsha, Hunan 410083, China
- Affiliated WuTaiShan Hospital of Medical College of Yangzhou University, Yangzhou Mental Health Centre, Yangzhou, Jiangsu 225003, China
- Affiliated Wuhan Mental Health Center, Huazhong University of Science and Technology, Wuhan, Hubei 430012, China
- Department of Psychiatry, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
- Mental Health Education and Counseling Center, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
- Key Laboratory of Cognition and Personality (Southwest University), Ministry of Education, Chongqing 400715, China
- Department of Psychology, Southwest University, Chongqing 400715, China
- Department of Magnetic Resonance Imaging, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Key Laboratory of Brain Functional Genomics (Ministry of Education), Affiliated Mental Health Center (East China Normal University), School of Psychology and Cognitive Science, East China Normal University, Shanghai 200062, China
- Department of Radiology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
- Peking University Sixth Hospital, Peking University Institute of Mental Health, National Health Commission Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University, Beijing 100191, China
- Department of Radiology, Huaxi MR Research Center, Institute of Radiology and Medical Imaging, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
- Psychoradiology Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
- Xiamen Key Lab of Psychoradiology and Neuromodulation, Department of Radiology, West China Xiamen Hospital of Sichuan University, Xiamen, Fujian 361022, China
- Affiliated Mental Health Center and Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310013, China
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei 112304, China
- Department of Education and Research, Taipei City Hospital, Taipei 103212, China
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
- Chongqing Key Laboratory of Neurobiology, Chongqing 400016, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Chinese Institute for Brain Research, Beijing 102206, China
Abstract
The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repository
Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.
ALICE1029/topography_MDD
ce1c5e766d572851c68b3b0552e93e90da73c40e, 11 May 2026Availability: 1 check, the latest on 30 September 2026: the link answers
- 30 September 2026: the link answers
61 files
- 1.Predict_brain_age/
s1.NMF/ , MATLAB, 13 liness0_script_CreatePrepData .m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 38 liness1_script_FuncInit_vol.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 10 liness2_script_SelRobustInit_ vol.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 52 liness3_script_FuncMvnmfL21p1 _func_vol.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 27 liness4_script_SaveResImg_vol .m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 39 liness5_name_network.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 218 lines, 1 matchsrc/ backNMF_u.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 295 linessrc/ backNMF_v.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 52 linessrc/ constructW_vol.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 25 linessrc/ createPrepData.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 62 linessrc/ dataPrepro.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 70 linessrc/ deployFuncInit_vol.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 68 linessrc/ deployFuncMvnmfL21p1_fun c_vol.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 64 linessrc/ dispSM_func.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 235 linessrc/ func_mMvNMF4fmri_l21p1_a rd_woSrcLoad.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 64 linessrc/ func_saveVolRes2Nii.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 67 linessrc/ func_saveVolRes2Nii_idv. m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 304 linessrc/ mMultiNMF_l21p1_ard.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 362 linessrc/ mMultiNMF_l21p1_ard_parf or.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 406 linessrc/ mNMF_sp.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 398 linessrc/ mNMF_sp_v.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 18 linessrc/ my_cifti.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 122 linessrc/ my_func_initialization_w oLoadSrc.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 14 linessrc/ my_vol.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 34 linessrc/ prepareFuncData_vol_func .m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 18 linessrc/ prepareFuncData_vol_func _single.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 33 linessrc/ read_cifti.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 11 linessrc/ read_coor.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 12 linessrc/ read_medial_wall_label.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 83 linessrc/ selRobustInit.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 82 linessrc/ vali_deploy.m - 1.Predict_brain_age/
s1.NMF/ , MATLAB, 235 linessrc/ vali_func.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 44 linesfunctions/ SVR_all.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 30 linesfunctions/ SVR_all_noco.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 107 linesfunctions/ pca_svr.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 109 linesfunctions/ pca_svr_noco.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 9 linesfunctions/ regress_out.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 102 liness1_index.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 225 liness2_predict.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 83 liness2_predict_loso.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 91 liness2_predict_mfd.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 162 liness2_predict_sex.m - 1.Predict_brain_age/
s2.brain_age/ , MATLAB, 218 liness3_system_predict.m - 2.Analyse_subtypes_brain
/ , Python, 39 linesfunctions/ brainsmash_inter.py - 2.Analyse_subtypes_brain
/ , MATLAB, 22 linesfunctions/ prepare_vars_for_norm_mo dels.m - 2.Analyse_subtypes_brain
/ , MATLAB, 22 linesfunctions/ vars_boot.m - 2.Analyse_subtypes_brain
/ , MATLAB, 22 linesfunctions/ vars_permut.m - 2.Analyse_subtypes_brain
/ , MATLAB, 114 linesfunctions/ x_GRF.m - 2.Analyse_subtypes_brain
/ , MATLAB, 341 liness1_BAG_topography_correl ation.m - 2.Analyse_subtypes_brain
/ , MATLAB, 365 liness2_trajectory_feature.m - 2.Analyse_subtypes_brain
/ , R, 80 liness3_gamlss_test.R - 3.Analyse_subtypes_clini
cal/ , Python, 144 linesFunctions/ cca.py - 3.Analyse_subtypes_clini
cal/ , MATLAB, 115 linesstep1_hamd_subscale_feat ure_generate.m - 3.Analyse_subtypes_clini
cal/ , Python, 49 linesstep2_pls_sub_topography .py - 3.Analyse_subtypes_clini
cal/ , MATLAB, 244 linesstep3_weight.m - 3.Analyse_subtypes_clini
cal/ , MATLAB, 178 linesstep7_treatment_CSU.m - 3.Analyse_subtypes_clini
cal/ , MATLAB, 141 linesstep7_treatment_system_C SU.m - 4.gene/
gen_surrogate_map_for g1z.py , Python, 11 lines - 4.gene/
s1_brainspan.m , MATLAB, 98 lines, 1 match - 4.gene/
s2_gene_PLS_analysis.m , MATLAB, 166 lines - README.md, Text, 73 lines
The paper's code and data availability statement is in the Data section.
Tracing map
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What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 60 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
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Code and data availability statement
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- no repository, dataset or request procedure was recognized in it
Read it in the paper: doi.org/10.1073/pnas.2519586123.
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Version 1, 30 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 33 authors, 5 keywords, 11 MeSH terms, 3 funders, 74 references.
Cite
This paper
Pang, C., Sun, X., Zhao, J., Liang, X., Sun, L., Lin, Q., Sun, J., Lu, X., Dong, Q., Zhang, L., Wang, X., Wei, D., Chen, Y., Liu, B., Huang, C.-C., Zheng, Y., Wu, Y., Chen, T., Cheng, Y., . . . Xia, M. (2026). Personalized functional topography-based multisite brain age prediction modeling reveals divergent neurodevelopment in major depression. Proceedings of the National Academy of Sciences of the United States of America, 123(11), e2519586123. https://
BibTeX
@article{pang2026persona
author = {Pang, Chenxuan and Sun, Xiaoyi and Zhao, Jianlong and Liang, Xinyuan and Sun, Lianglong and Lin, Qixiang and Sun, Jinrong and Lu, Xiaowen and Dong, Qiangli and Zhang, Liang and Wang, Xiaoqin and Wei, Dongtao and Chen, Yuan and Liu, Bangshan and Huang, Chu-Chung and Zheng, Yanting and Wu, Yankun and Chen, Taolin and Cheng, Yuqi and Xu, Xiufeng and Gong, Qiyong and Si, Tianmei and Qiu, Shijun and Lin, Ching-Po and Cheng, Jingliang and Tang, Yanqing and Wang, Fei and Qiu, Jiang and Xie, Peng and Li, Lingjiang and He, Yong and {DIDA-MDD Working Group} and Xia, Mingrui},
title = {{Personalized functional topography-based multisite brain age prediction modeling reveals divergent neurodevelopment in major depression}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2026},
month = mar,
volume = {123},
number = {11},
pages = {e2519586123},
publisher = {National Academy of Sciences},
issn = {0027-8424},
doi = {10.1073/
url = {https://
pmid = {41811439},
pmcid = {PMC12994210}
}
RIS
TY - JOUR
AU - Pang, Chenxuan
AU - Sun, Xiaoyi
AU - Zhao, Jianlong
AU - Liang, Xinyuan
AU - Sun, Lianglong
AU - Lin, Qixiang
AU - Sun, Jinrong
AU - Lu, Xiaowen
AU - Dong, Qiangli
AU - Zhang, Liang
AU - Wang, Xiaoqin
AU - Wei, Dongtao
AU - Chen, Yuan
AU - Liu, Bangshan
AU - Huang, Chu-Chung
AU - Zheng, Yanting
AU - Wu, Yankun
AU - Chen, Taolin
AU - Cheng, Yuqi
AU - Xu, Xiufeng
AU - Gong, Qiyong
AU - Si, Tianmei
AU - Qiu, Shijun
AU - Lin, Ching-Po
AU - Cheng, Jingliang
AU - Tang, Yanqing
AU - Wang, Fei
AU - Qiu, Jiang
AU - Xie, Peng
AU - Li, Lingjiang
AU - He, Yong
AU - DIDA-MDD Working Group
AU - Xia, Mingrui
TI - Personalized functional topography-based multisite brain age prediction modeling reveals divergent neurodevelopment in major depression
T2 - Proceedings of the National Academy of Sciences of the United States of America
J2 - Proc Natl Acad Sci U S A
PY - 2026
DA - 2026/
VL - 123
IS - 11
SP - e2519586123
SN - 0027-8424
PB - National Academy of Sciences
DO - 10.1073/
UR - https://
LA - en
ER -
CSL-JSON
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