GeneFriends: gene co-expression databases and tools for humans and model organisms.
Priyanka RainaRodrigo GuineaKasit ChatsirisupachaiInês LopesZoya FarooqCristina GuineaCsaba-Attila SolyomJoão Pedro de MagalhãesPublished in: Nucleic acids research (2022)
Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring the relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have now updated the GeneFriends database and website. Here, we present the new version of GeneFriends, which includes gene and transcript co-expression networks based on RNA-seq data from 46 475 human and 34 322 mouse samples. The new database also encompasses tissue-specific gene co-expression networks for 20 human and 21 mouse tissues, dataset-specific gene co-expression maps based on TCGA and GTEx projects and gene co-expression networks for additional seven model organisms (fruit fly, zebrafish, worm, rat, yeast, cow and chicken). GeneFriends is freely available at http://www.genefriends.org/.
Keyphrases
- poor prognosis
- genome wide identification
- rna seq
- genome wide
- copy number
- single cell
- long non coding rna
- type diabetes
- dna methylation
- genome wide analysis
- electronic health record
- gene expression
- binding protein
- emergency department
- oxidative stress
- metabolic syndrome
- human immunodeficiency virus
- machine learning
- hepatitis c virus
- men who have sex with men
- deep learning
- artificial intelligence
- induced pluripotent stem cells
- wild type