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

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 experiments. 

Table S8: Group membership for each one of the nodes in each one of the selected networks according to the SBM that best describes the observed network topology. Each column shows the group membership for each level in a SBM block hierarchy. Our analysis is in the second most coarse-grained level (level 1).

TableS8a_max_AUFE_SBM.csv
TableS8b_max_PFE_SBM.csv
TableS8c_middle_AUFE_PFE_SBM.csv

TableS9_glp_gs_datasets.pdf - list of datasets used for defining functional clusters.

TableS14a_glp_l1_vs_fem_l1_lifespan_assay.xlsx - Day13 survival of fem-3(q20)ts vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1

TableS14b_glp_l1_vs_glp_l4_lifespan_assay.xlsx - Day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L4 vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1

TableS15a_glp1_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of glp-1(e2144)ts;rrf-3(pk1426)

TableS15b_fem3_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of fem-3(q20)ts

TableS17_input_regulators_annotated.csv - list input regulators used as input for Network Inference Tools annotated by source type (2nd column): GenAge, known transcription factors (TF) and gene with high variability in the gene expression time series (HV). The third column lists whether that regulator has an orthologue in human (y) according to WormBase (v 278).

TableS20_epistasis_lifespan_data.xlsx - Epistasis lifespan data of glp-1(e2144)ts

All the image (TIF) files represent representative images in the following genetic backgrounds (below) that have been treated 

with empty vector (EV) or RNAi against the gene highlighted in the title of the image. See methods section for details. 

femliu1: 

fem-3(q20)ts.; dhs-3p::dhs-3::gfp

femsod3:

fem-3(q20)ts.; sod-3p::gfp

glp1lgg1:

glp-1(e2144); lgg-1p:lgg-1:gfp