Schema for lincRNA RNA-Seq - lincRNA RNA-Seq reads expression abundances
  Database: hg38    Primary Table: lincRNAsCTAdipose    Row Count: 21,532   Data last updated: 2015-04-13
Format description: lincRNA reads expression table by cell type
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Human chromosome or FPC contig
chromStart 16857int(10) unsigned range Start position in chromosome
chromEnd 17751int(10) unsigned range End position in chromosome
name TCONS_l2_00002360varchar(255) values Name of item
score 704int(10) unsigned range Score from 0-1000
rawScore 5.2499float range Raw Signal Score
log2RawScore 2.524float range log2 of raw score

Sample Rows
 
binchromchromStartchromEndnamescorerawScorelog2RawScore
585chr11685717751TCONS_l2_000023607045.24992.524
585chr11685719759TCONS_l2_000023617045.24992.524
585chr11685729370TCONS_l2_000023627045.24992.524
585chr11685729961TCONS_l2_000023637045.24992.524
585chr11723229370TCONS_l2_000023647045.24992.524
585chr11760529370TCONS_l2_000023657045.24992.524
585chr189294120932TCONS_l2_000023676484.23512.243
585chr18955091105TCONS_l2_000023696484.23512.243
585chr191373112736TCONS_l2_000009576484.23512.243
585chr192229129217TCONS_l2_000023706484.23512.243

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

lincRNA RNA-Seq (lincRNAsAllCellTypeTopView) Track Description
 

Description

This track displays the Human Body Map lincRNAs (large intergenic non coding RNAs) and TUCPs (transcripts of uncertain coding potential), as well as their expression levels across 22 human tissues and cell lines. The Human Body Map catalog was generated by integrating previously existing annotation sources with transcripts that were de-novo assembled from RNA-Seq data. These transcripts were collected from ~4 billion RNA-Seq reads across 24 tissues and cell types.

Expression abundance was estimated by Cufflinks (Trapnell et al., 2010) based on RNA-Seq. Expression abundances were estimated on the gene locus level, rather than for each transcript separately and are given as raw FPKM. The prefixes tcons_ and tcons_l2_ are used to describe lincRNAs and TUCP transcripts, respectively. Specific details about the catalog generation and data sets used for this study can be found in Cabili et al (2011). Extended characterization of each transcript in the human body map catalog can be found at the Human lincRNA Catalog website.

Expression abundance scores range from 0 to 1000, and are displayed from light blue to dark blue respectively:

01000

Credits

The body map RNA-Seq data was kindly provided by the Gene Expression Applications research group at Illumina.

References

Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25(18):1915-27. PMID: 21890647; PMC: PMC3185964

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. PMID: 20436464; PMC: PMC3146043