Cattle condition-independent Gene Co-expression Network (CGCN)
Query for genes that are associated with known expressed genes

DATA DESCRIPTION

RAW DATA: Curated gene expression datasets of original Series and Platform records from the NCBI Gene Expression Omnibus (GEO) repository.

PROCESS: Weighted correlation network analysis ( Langfelder P, Horvath S: WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics 2008, 9:559) was used to identify similarity between genes expression values under different tissues and experimental conditions. Briefly, adjacency matrix was formed based on correlation between gene expression values. Subsequently, the adjacency matrix raised to power 7 based on network scale free properties and used to calculate similarity between gene expression values based on "Topological Overlap Measure (TOM)". Theoretically, TOM measure varies between 0 and 1. It should be noted that this measure calculated after raising correlations to power 7, so its values are expected to be small. For example TOM values more than 0.01 imply tight interconnections between genes.

OUTCOME: 137,887,921 connectivities were identified among 16,608 probe sets which represent 11,125 genes. The genes identified with "guilt-by-association" assumption helps to provide clues for related genes that might worth further investigation for their roles regulating certain phenotypes.

USE THE DATA

  • This data set is available for download at the NAGRP Shared Data Repository
    (File name: "Related_genes_by_TOM_connectivity.txt.gz"
  • The data set may be queried for user targeted genes by the following steps:
Step 1: Search by gene (symbol, name, id), probe name, or a cut-off TOM connectivity threshold (how closely genes are related).

Step 2: Review the preliminary search results summary, decide if you want to download the data

Step 3: Download data to visualize the network relationships with Cytoscape, Miru or similar software


Step 1

Search the data set to look for genes that might be associated with those that were differentially expressed. Note when you have search terms in multiple fields below, they will be Boolean AND'ed.
by probe ID: e.g. Bt.10018.2.A1_at
by gene name/symbol/id: e.g. ENSBTAG00000010349; 281250 (NCBI Gene ID);      synthase (Gene name); CD9 (Gene symbol);
TOM value greater than: e.g. 0.01 (between 1 and 0; larger value
     represents stronger connectivity*)
* Please refer to this TOM scores frequency distribution to best choose your TOM value cut-off value.
Reference:
Hamid Beiki, Ardeshir Nejati-Javaremi, Abbas Pakdel, Ali Masoudi-Nejad, Zhi-Liang Hu and James M Reecy. (2016). Large-scale gene co-expression network as a source of functional annotation for cattle genes. BMC Genomics, 2016, 17:846.
Supplementary data:
All data are deposited at and available from Open Science Framework (OSF) website.

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