Non-redundant compendium of human ncRNA genes in GeneCards

被引：32

作者：

Belinky, Frida ^{[1
]}

Bahir, Iris ^{[1
]}

Stelzer, Gil ^{[1
]}

Zimmerman, Shahar ^{[1
]}

Rosen, Naomi ^{[1
]}

Nativ, Noam ^{[1
]}

Dalah, Irina ^{[1
]}

Stein, Tsippi Iny ^{[1
]}

Rappaport, Noa ^{[1
]}

Mituyama, Toutai ^{[2
]}

Safran, Marilyn ^{[1
,3
]}

Lancet, Doron ^{[1
]}

机构：

[1] Weizmann Inst Sci, Dept Mol Genet, IL-76100 Rehovot, Israel

[2] Adv Ind Sci & Technol AIST, Computat Biol Res Ctr CBRC, Koto Ku, Tokyo 1350064, Japan

[3] Weizmann Inst Sci, Dept Biol Serv, IL-76100 Rehovot, Israel

来源：

BIOINFORMATICS | 2013年 / 29卷 / 02期

关键词：

TRANSCRIPTIONAL NOISE; NONCODING RNAS; HUMAN GENOME; DATABASE; ANNOTATION; PIRNA; RESOURCES; SEQUENCES; REGIONS;

D O I：

10.1093/bioinformatics/bts676

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Non-coding RNA (ncRNA) genes are increasingly acknowledged for their importance in the human genome. However, there is no comprehensive non-redundant database for all such human genes. Results: We leveraged the effective platform of GeneCards, the human gene compendium, together with the power of fRNAdb and additional primary sources, to judiciously unify all ncRNA gene entries obtainable from 15 different primary sources. Overlapping entries were clustered to unified locations based on an algorithm employing genomic coordinates. This allowed GeneCards' gamut of relevant entries to rise similar to 5-fold, resulting in similar to 80 000 human non-redundant ncRNAs, belonging to 14 classes. Such 'grand unification' within a regularly updated data structure will assist future ncRNA research.

引用

页码：255 / 261

页数：7

共 57 条

[1] A novel class of small RNAs bind to MILI protein in mouse testes [J].

Aravin, Alexei ;

Gaidatzis, Dimos ;

Pfeffer, Sebastien ;

Lagos-Quintana, Mariana ;

Landgraf, Pablo ;

Iovino, Nicola ;

Morris, Patricia ;

Brownstein, Michael J. ;

Kuramochi-Miyagawa, Satomi ;

Nakano, Toru ;

Chien, Minchen ;

Russo, James J. ;

Ju, Jingyue ;

Sheridan, Robert ;

Sander, Chris ;

Zavolan, Mihaela ;

Tuschl, Thomas .

NATURE, 2006, 442 (7099) :203-207

[2] RNAcentral: A vision for an international database of RNA sequences [J].

Bateman, Alex ;

Agrawal, Shipra ;

Birney, Ewan ;

Bruford, Elspeth A. ;

Bujnicki, Janusz M. ;

Cochrane, Guy ;

Cole, James R. ;

Dinger, Marcel E. ;

Enright, Anton J. ;

Gardner, Paul P. ;

Gautheret, Daniel ;

Griffiths-Jones, Sam ;

Harrow, Jen ;

Herrero, Javier ;

Holmes, Ian H. ;

Huang, Hsien-Da ;

Kelly, Krystyna A. ;

Kersey, Paul ;

Kozomara, Ana ;

Lowe, Todd M. ;

Marz, Manja ;

Moxon, Simon ;

Pruitt, Kim D. ;

Samuelsson, Tore ;

Stadler, Peter F. ;

Vilella, Albert J. ;

Vogel, Jan-Hinnerk ;

Williams, Kelly P. ;

Wright, Mathew W. ;

Zwieb, Christian .

RNA, 2011, 17 (11) :1941-1946

[3]

Benson DA, 2013, NUCLEIC ACIDS RES, V41, pD36, DOI [10.1093/nar/gkn723, 10.1093/nar/gkp1024, 10.1093/nar/gkw1070, 10.1093/nar/gkr1202, 10.1093/nar/gkx1094, 10.1093/nar/gkl986, 10.1093/nar/gkq1079, 10.1093/nar/gks1195, 10.1093/nar/gkg057]

[4] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[5] Transcription: Surprising role for an elusive small nuclear RNA [J].

Blencowe, BJ .

CURRENT BIOLOGY, 2002, 12 (04) :R147-R149

[6] NONCODE v3.0: integrative annotation of long noncoding RNAs [J].

Bu, Dechao ;

Yu, Kuntao ;

Sun, Silong ;

Xie, Chaoyong ;

Skogerbo, Geir ;

Miao, Ruoyu ;

Xiao, Hui ;

Liao, Qi ;

Luo, Haitao ;

Zhao, Guoguang ;

Zhao, Haitao ;

Liu, Zhiyong ;

Liu, Changning ;

Chen, Runsheng ;

Zhao, Yi .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D210-D215

[7] MicroRNA functions [J].

Bushati, Natascha ;

Cohen, Stephen M. .

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, 2007, 23 :175-205

[8] The transcriptional landscape of the mammalian genome [J].

Carninci, P ;

Kasukawa, T ;

Katayama, S ;

Gough, J ;

Frith, MC ;

Maeda, N ;

Oyama, R ;

Ravasi, T ;

Lenhard, B ;

Wells, C ;

Kodzius, R ;

Shimokawa, K ;

Bajic, VB ;

Brenner, SE ;

Batalov, S ;

Forrest, ARR ;

Zavolan, M ;

Davis, MJ ;

Wilming, LG ;

Aidinis, V ;

Allen, JE ;

Ambesi-Impiombato, X ;

Apweiler, R ;

Aturaliya, RN ;

Bailey, TL ;

Bansal, M ;

Baxter, L ;

Beisel, KW ;

Bersano, T ;

Bono, H ;

Chalk, AM ;

Chiu, KP ;

Choudhary, V ;

Christoffels, A ;

Clutterbuck, DR ;

Crowe, ML ;

Dalla, E ;

Dalrymple, BP ;

de Bono, B ;

Della Gatta, G ;

di Bernardo, D ;

Down, T ;

Engstrom, P ;

Fagiolini, M ;

Faulkner, G ;

Fletcher, CF ;

Fukushima, T ;

Furuno, M ;

Futaki, S ;

Gariboldi, M .

SCIENCE, 2005, 309 (5740) :1559-1563

[9] Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs [J].

Cawley, S ;

Bekiranov, S ;

Ng, HH ;

Kapranov, P ;

Sekinger, EA ;

Kampa, D ;

Piccolboni, A ;

Sementchenko, V ;

Cheng, J ;

Williams, AJ ;

Wheeler, R ;

Wong, B ;

Drenkow, J ;

Yamanaka, M ;

Patel, S ;

Brubaker, S ;

Tammana, H ;

Helt, G ;

Struhl, K ;

Gingeras, TR .

CELL, 2004, 116 (04) :499-509

[10] piR-823, a novel non-coding small RNA, demonstrates in vitro and in vivo tumor suppressive activity in human gastric cancer cells [J].

Cheng, Jia ;

Deng, Hongxia ;

Xiao, Bingxiu ;

Zhou, Hui ;

Zhou, Fei ;

Shen, Zhisen ;

Guo, Junming .

CANCER LETTERS, 2012, 315 (01) :12-17

← 1 2 3 4 5 6 →