Tyler Weirick1, David John1, Stefanie Dimmeler1, Shizuka Uchida1. 1. Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt and German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main, Germany.
Abstract
MOTIVATION: Increasing evidences suggest that most of the genome is transcribed into RNAs, but many of them are not translated into proteins. All those RNAs that do not become proteins are called 'non-coding RNAs (ncRNAs)', which outnumbers protein-coding genes. Interestingly, these ncRNAs are shown to be more tissue specifically expressed than protein-coding genes. Given that tissue-specific expressions of transcripts suggest their importance in the expressed tissue, researchers are conducting biological experiments to elucidate the function of such ncRNAs. Owing greatly to the advancement of next-generation techniques, especially RNA-seq, the amount of high-throughput data are increasing rapidly. However, due to the complexity of the data as well as its high volume, it is not easy to re-analyze such data to extract tissue-specific expressions of ncRNAs from published datasets. RESULTS: Here, we introduce a new knowledge database called 'C-It-Loci', which allows a user to screen for tissue-specific transcripts across three organisms: human, mouse and zebrafish. C-It-Loci is intuitive and easy to use to identify not only protein-coding genes but also ncRNAs from various tissues. C-It-Loci defines homology through sequence and positional conservation to allow for the extraction of species-conserved loci. C-It-Loci can be used as a starting point for further biological experiments. AVAILABILITY AND IMPLEMENTATION: C-It-Loci is freely available online without registration at http://c-it-loci.uni-frankfurt.de. CONTACT: uchida@med.uni-frankfurt.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Increasing evidences suggest that most of the genome is transcribed into RNAs, but many of them are not translated into proteins. All those RNAs that do not become proteins are called 'non-coding RNAs (ncRNAs)', which outnumbers protein-coding genes. Interestingly, these ncRNAs are shown to be more tissue specifically expressed than protein-coding genes. Given that tissue-specific expressions of transcripts suggest their importance in the expressed tissue, researchers are conducting biological experiments to elucidate the function of such ncRNAs. Owing greatly to the advancement of next-generation techniques, especially RNA-seq, the amount of high-throughput data are increasing rapidly. However, due to the complexity of the data as well as its high volume, it is not easy to re-analyze such data to extract tissue-specific expressions of ncRNAs from published datasets. RESULTS: Here, we introduce a new knowledge database called 'C-It-Loci', which allows a user to screen for tissue-specific transcripts across three organisms: human, mouse and zebrafish. C-It-Loci is intuitive and easy to use to identify not only protein-coding genes but also ncRNAs from various tissues. C-It-Loci defines homology through sequence and positional conservation to allow for the extraction of species-conserved loci. C-It-Loci can be used as a starting point for further biological experiments. AVAILABILITY AND IMPLEMENTATION: C-It-Loci is freely available online without registration at http://c-it-loci.uni-frankfurt.de. CONTACT: uchida@med.uni-frankfurt.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Dinesh Devadoss; Christopher Long; Raymond J Langley; Marko Manevski; Madhavan Nair; Michael A Campos; Glen Borchert; Irfan Rahman; Hitendra S Chand Journal: Am J Respir Cell Mol Biol Date: 2019-12 Impact factor: 6.914
Authors: Jian Jun Jin; Wei Lv; Pan Xia; Zai Yan Xu; An Dai Zheng; Xiao Jing Wang; Shan Shan Wang; Rui Zeng; Hong Mei Luo; Guo Liang Li; Bo Zuo Journal: Proc Natl Acad Sci U S A Date: 2018-10-02 Impact factor: 11.205