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

Description

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…

Description from Zenodo, shortened.

Files (57)

• XLSXTableS15b_fem3_in_vivo_fluorescence_data.xlsx13 kB
• CSVTableS17_input_regulators_annotated.csv32 kB
• XLSXTableS18_strain_primer_list.xlsx109 kB
• CSVTableS19_nonvariable_genes.csv38 kB
• XLSXTableS20_epistasis_lifespan_data.xlsx14 kB
• CSVTableS4_inferred_networks.csv5 kB
• XLSXTableS5_consensus_network_member.xlsx6.9 kB
• TXTTableS6a_max_AUFE_GRN.txt4.4 MB
• XLSXTableS16_qRTPCR_gene_interaction_network.xlsx589 kB
• TXTTableS6b_max_PFE_GRN.txt3.9 MB
• TXTTableS6c_middle_AUFE_PFE_GRN.txt3.9 MB
• PDFTableS9_glp_gs_datasets.pdf174 kB
• PDFSupplementary Tables guide.pdf70 kB
• CSVTableS7_qRTPCR_ddCt_network_accuracy.csv215 kB
• CSVTableS8c_SBM_middle_PFE_AUFE_network.csv217 kB
• CSVTableS8a_SBM_max_AUFE_network.csv430 kB
• XLSXTableS10_first_screen_lifespan_assay.xlsx113 kB
• CSVTableS8b_SBM_max_PFE_network.csv205 kB
• CSVTableS11_glp_essential_genes.csv5.5 kB
• TIFfem3sod3_scd-3.tif116 MB
• XLSXTableS12_second_screen_lifespan_assay.xlsx112 kB
• XLSXTableS13_orthologues_new_ageing_genes.xlsx12 kB
• XLSXTableS14a_glp_l1_vs_fem_l1_lifespan_assay.xlsx17 kB
• XLSXTableS14b_glp_l1_vs_glp_l4_lifespan_assay.xlsx68 kB
• XLSXTableS15a_glp1_in_vivo_fluorescence_data.xlsx82 kB
• TIFglp1lgg1_HMG1.2.tif44 MB
• TIFfem3sod3_pqm-1.tif116 MB
• TIFfem3sod3_somi1.tif116 MB
• TIFfem3sod3_daf16.tif116 MB
• TIFfem3sod3_attf3.tif116 MB
• TIFfem3sod3_age1.tif116 MB
• TIFfem3liu1_zpga1.tif116 MB
• TIFfem3liu1_sup-37.tif116 MB
• TIFglp1lgg1_EV.tif44 MB
• TIFfem3liu1_somi-1.tif116 MB
• TIFglp1lgg1_DAF16.tif44 MB
• TIFfem3liu1_sdc-3.tif116 MB
• TIFglp1lgg1_C27A12.2.tif44 MB
• TIFfem3liu1_pqm1.tif116 MB
• TIFglp1lgg1_B0261.1.tif44 MB
• TIFfem3liu1_nduf-6.tif116 MB
• TIFfem3liu1_EV.tif116 MB
• TIFfem3liu1_dnj11.tif116 MB
• TIFfem3liu1_daf16.tif116 MB
• TIFglp1lgg1_ATTF6.tif44 MB
• TIFglp1lgg1_LIN13.tif44 MB
• TIFglp1lgg1_SDC3.tif44 MB
• TIFfem3sod3_hmbx1.tif116 MB
• TIFfem3sod3_nduf6.tif116 MB
• TIFglp1lgg1_ISW-1.tif44 MB
• TIFfem3sod3_EV.tif116 MB
• TIFfem3sod3_zpga-1.tif116 MB
• TIFfem3sod3_sup37.tif116 MB
• TIFfem3sod3_dnj11.tif116 MB
• TIFfem3liu1_attf3.tif116 MB
• TIFfem3liu1_age 1.tif116 MB
• TIFfem3liu1_hmbx1.tif116 MB

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