FARNA – knowledgebase of inferred functions of non-coding RNA transcripts

Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, researchers from the King Abdullah University of Science and Technology present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human.

Brief description of the pipeline used to infer cell/tissue-specific
functions of miRNA and lncRNA transcripts


First, FANTOM5 CAGE data for primary cells and tissues was collected. The miRNA, lncRNA, TF and TcoF transcripts that are expressed in different cells/tissues were used for further analysis in cell/tissue-specific manner. The TF binding site (TFBS) models from TRANSFAC and HOCOMOCO databases were used to predict TFBSs on promoter regions of miRNA and lncRNA transcripts. Only TFs and their associated TcoFs that are expressed in the considered cell/tissue together with the ncRNA transcript are used to infer statistically significant cell/tissue-specific functions of the transcript.

Availability – FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna

Alam T, Uludag M, Essack M, Salhi A, Ashoor H, Hanks JB, Kapfer C, Mineta K, Gojobori T, Bajic VB. (2016) FARNA: knowledgebase of inferred functions of non-coding RNA transcripts NAR [Epub ahead of print]. [article]

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