giant_tissue_networks — Human tissue-specific functional gene networks (GIANT/HumanBase, 2015)
- Description
Functional gene networks of 144 human tissues and cell types, from GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), now part of HumanBase (Flatiron Institute). Nodes are human genes, and an edge between two genes is weighted by the probability that they are functionally related (e.g. take part in the same biological process) in the tissue. The networks were built by integrating about 38,000 genome-scale experiments (gene expression data sets, protein-protein interactions, transcription factor binding, chemical and genetic perturbations, microRNA targets) with a Bayesian approach: for each tissue, the gold standard of related genes was restricted to those expressed in the tissue (from tissue-specific expression data in the literature and the Human Protein Reference Database), so that the data sets informative of that tissue are weighted accordingly. The tissues and cell types are terms of the BRENDA Tissue Ontology (BTO), and include e.g. organs (
kidney,liver,heart), brain regions (hippocampus,substantia_nigra), cell types (neuron,t_lymphocyte,hepatocyte) and fluids (blood_plasma); the networkglobalis the tissue-naive network, built with the gold standard of all genes.The complete networks give a probability for every pair of about 25,000 genes (291 GB of files). The networks here are the "top edges" networks provided by HumanBase: they contain only the edges whose probability exceeds the prior probability of a functional relationship, 0.1, which leaves between about 30 and 280 million edges per network (e.g. 39 million for
global, 62 million forkidney, 283 million forcochlea). Each network contains the genes with at least one such edge. The probabilities assume this prior (as the networks shown on the HumanBase website). The gold standards of the tissues (the positive and negative examples used for training) are not included.The networks have the following properties:
- (Node)
entrez_id: the NCBI Entrez Gene identifier of the gene. - (Node)
symbol: the official symbol of the gene, e.g.TP53, from the current NCBI Gene database (empty if the identifier was discontinued since). - (Node)
description: the name of the gene, e.g.tumor protein p53(empty if the identifier was discontinued). - (Edge)
weight: the posterior probability of a functional relationship between the two genes in the tissue (between 0.1 and 1). - (Node)
tissue(graph): the name of the tissue or cell type in the BRENDA Tissue Ontology (globalfor the global network). - (Node)
bto_id(graph): the identifier of the tissue or cell type in the BRENDA Tissue Ontology, e.g.BTO:0000671(empty for the global network).
- (Node)
- Tags
- Biological Genetic Weighted Metadata
- Citation
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- C. S. Greene, A. Krishnan, A. K. Wong, E. Ricciotti, R. A. Zelaya, D. S. Himmelstein, R. Zhang, B. M. Hartmann, E. Zaslavsky, S. C. Sealfon, D. I. Chasman, G. A. FitzGerald, K. Dolinski, T. Grosser, O. G. Troyanskaya, "Understanding multicellular function and disease with human tissue-specific networks." Nature Genetics 47, 569-576 (2015) 10.1038/ng.3259 Sci-Hub
- Upstream URL OK
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https://hb.flatironinstitute.org/download
https://www.ncbi.nlm.nih.gov/gene - Networks
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Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
- $\left<k\right>$
- Mean degree
- $\sigma_k$
- Standard deviation of the degrees
- $\lambda_h$
- Largest eigenvalue of the Hashimoto (non-backtracking) matrix
- $\tau$
- Random walk mixing time
- $r$
- Degree assortativity
- $c$
- Global clustering coefficient
- $\oslash$
- (Pseudo-) diameter
- $S$
- Relative size of the largest component
- NPs
- Node properties
- EPs
- Edge properties