Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Supplementary Tables

Описание

This repository contains the Supplementary Tables for Suriyalaksh et al. Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes. The list of table files can be found in Supplementary Tables guide.pdf Tables S1, S2 and S3 corresponding to physical gene-gene interaction data are in a separate repository doi:10.5281/zenodo.4382337 Details about some of the Supplementary tables: TableS4 inferred networks.csv - list of inferred GRNs for specified input combinations (set of input regulators, length of the time sequence, NI tool and prior used). TableS5 consensus network member.xlsx - list of groups of topologically similar GRNs (from Table S4) Table S6: edge lists (source,target) for each one of the three consensus networks selected according to the GS validation metrics: middle PFE/AUFE, max AUFE, max PFE. TableS6a max AUFE GRN.txt - max AUFE; largest network - this is the one we used in the main analysis and discussion TableS6b max PFE GRN.xt - max PFE TableS6c middle AUFE PFE GRN.txt - middle PFE/AUFE TableS7 qRTPCR ddCt network accuracy.csv - gene expression count differences for RNAi knockdown GRN validation…

Описание из Zenodo, сокращённое.

Файлы (57)

• XLSXTableS15b_fem3_in_vivo_fluorescence_data.xlsx13 кБ
• CSVTableS17_input_regulators_annotated.csv32 кБ
• XLSXTableS18_strain_primer_list.xlsx109 кБ
• CSVTableS19_nonvariable_genes.csv38 кБ
• XLSXTableS20_epistasis_lifespan_data.xlsx14 кБ
• CSVTableS4_inferred_networks.csv5 кБ
• XLSXTableS5_consensus_network_member.xlsx6,9 кБ
• TXTTableS6a_max_AUFE_GRN.txt4,4 МБ
• XLSXTableS16_qRTPCR_gene_interaction_network.xlsx589 кБ
• TXTTableS6b_max_PFE_GRN.txt3,9 МБ
• TXTTableS6c_middle_AUFE_PFE_GRN.txt3,9 МБ
• PDFTableS9_glp_gs_datasets.pdf174 кБ
• PDFSupplementary Tables guide.pdf70 кБ
• CSVTableS7_qRTPCR_ddCt_network_accuracy.csv215 кБ
• CSVTableS8c_SBM_middle_PFE_AUFE_network.csv217 кБ
• CSVTableS8a_SBM_max_AUFE_network.csv430 кБ
• XLSXTableS10_first_screen_lifespan_assay.xlsx113 кБ
• CSVTableS8b_SBM_max_PFE_network.csv205 кБ
• CSVTableS11_glp_essential_genes.csv5,5 кБ
• TIFfem3sod3_scd-3.tif116 МБ
• XLSXTableS12_second_screen_lifespan_assay.xlsx112 кБ
• XLSXTableS13_orthologues_new_ageing_genes.xlsx12 кБ
• XLSXTableS14a_glp_l1_vs_fem_l1_lifespan_assay.xlsx17 кБ
• XLSXTableS14b_glp_l1_vs_glp_l4_lifespan_assay.xlsx68 кБ
• XLSXTableS15a_glp1_in_vivo_fluorescence_data.xlsx82 кБ
• TIFglp1lgg1_HMG1.2.tif44 МБ
• TIFfem3sod3_pqm-1.tif116 МБ
• TIFfem3sod3_somi1.tif116 МБ
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• TIFfem3sod3_attf3.tif116 МБ
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• TIFfem3liu1_zpga1.tif116 МБ
• TIFfem3liu1_sup-37.tif116 МБ
• TIFglp1lgg1_EV.tif44 МБ
• TIFfem3liu1_somi-1.tif116 МБ
• TIFglp1lgg1_DAF16.tif44 МБ
• TIFfem3liu1_sdc-3.tif116 МБ
• TIFglp1lgg1_C27A12.2.tif44 МБ
• TIFfem3liu1_pqm1.tif116 МБ
• TIFglp1lgg1_B0261.1.tif44 МБ
• TIFfem3liu1_nduf-6.tif116 МБ
• TIFfem3liu1_EV.tif116 МБ
• TIFfem3liu1_dnj11.tif116 МБ
• TIFfem3liu1_daf16.tif116 МБ
• TIFglp1lgg1_ATTF6.tif44 МБ
• TIFglp1lgg1_LIN13.tif44 МБ
• TIFglp1lgg1_SDC3.tif44 МБ
• TIFfem3sod3_hmbx1.tif116 МБ
• TIFfem3sod3_nduf6.tif116 МБ
• TIFglp1lgg1_ISW-1.tif44 МБ
• TIFfem3sod3_EV.tif116 МБ
• TIFfem3sod3_zpga-1.tif116 МБ
• TIFfem3sod3_sup37.tif116 МБ
• TIFfem3sod3_dnj11.tif116 МБ
• TIFfem3liu1_attf3.tif116 МБ
• TIFfem3liu1_age 1.tif116 МБ
• TIFfem3liu1_hmbx1.tif116 МБ

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