Cumulative coverage of sRNAs giving rise to a single alignment in step 4 was computed using bedtools in a window of 1000 nt centered on GENCODE
v24 polyA sites.
Gonzalez et al., "GENCODE
: the reference human genome annotation for the ENCODE Project," Genome Research, vol.
Nevertheless, the Gencode
project aims to find all the protein-coding genes and the many permutations of those genes that can produce a dizzying number of proteins.
One root - from Rice to GML to my basic SGML invention - joined at the base of the trunk by the other - Tunnicliffe to Scharpf and GenCode
. The trunk, of course, is the extraordinary 8-year effort to develop ISO 8879, involving hundreds of people from all over the world.
In the human genome, 15,787 lncRNA transcripts from 14,470 lncRNA genes have been identified, while the GENCODE
annotation is constantly being updated [20, 21].
The lncRNAs are carefully constructed using the quality-controlled, public transcriptome databases (RefSeq, UCSC Known Genes, lncRNAWiki, LNCipedia, NONCODE v4, fRNAdb v3.4, Broad lincRNA, GENCODE
, etc.), as well as landmark publications.
Annotations can be gene-based (users can select the gene definition system; RefSeq, UCSC, ENSEMBL, GENCODE
, etc.), region-based (transcription factor binding sites, DNAse I hypersensitivity sites, ENCODEmethylation sites, segmental duplication sites, DGV sites, etc.), filter-based (e.g., using only variants reported in dbSNP, or only variants with MAF > 1%), or based on any of many other user-driven functionalities.
In the early 1980s, the Graphics Communications Association (GCA), an industry group, initiated a movement to create a standard markup language called "GenCode
," which typesetting vendors would all be persuaded to accept as input.
With the ending of phase I of the 1000 genomes project, we are facing the fact that human genome has on average around 3.7 million single nucleotide polymorphisms (SNPs) of which 24 000 are in GENCODE
regions [1, 2].
cerevisiae, are collected from GENCODE
and Ensembl database.
6889 (93.3%) were identified in Gencode
v19 lncRNA annotation; the remaining 341 were novel lncRNAs, including 300 (87.98%) long intergenic ncRNAs (lincRNAs) and 41 (12.02%) antisense lncRNAs (Figures 2(c) and 2(d)).
LncRNAs with enhancer-like functions (lncRNA-a) were identified with GENCODE