LncRNA Data Page - Gencode Version 7 Annotations

These data are described in the publication:

The GENCODE v7 catalogue of human long non-coding RNAs: Analysis of their gene structure, evolution and expression

Derrien et al

On this page you will find various data files relating to our work on lncRNA. 

Please note:

1) All coordinates refer to human genome version GRCh37 (hg19).

2) The genesets here are all from GENCODE version 7, unless stated otherwise.

3) Original GENCODE annotations can be found here: http://www.gencodegenes.org/releases/7.html

4) This page is maintained by Rory Johnson (rory.johnson@crg.eu; www.roryjohnson.org). Please contact me with any questions or requests regarding this data.

Compendium of GENCODE v7 lncRNA Annotation: Supplementary Table 1

This table summarises almost everything we know about the Gencode v7 lncRNA catalogue.

• Supplementary table (.txt format)

• Supplementary table (.xls format)

• Supplementary table (.csv format)

This table contains over 60 metrics (merged in 32 fields) computed for 14,880 Gencode LncRNAs transcripts :

# - 1 LncRNA_GeneId : lncRNA gene ID (v7)

# - 2 LncRNA_Txid : lncRNA transcript ID (v7)

# - 3 hg19_coordinates : genome coordinates (chr:start-stop)

# - 4 No_Exons : number of exons of the transcript

# - 5 LncRNA_tx_size : total length of concatenated exons

# - 6 LncRNA_IntronS_size : total length of all introns

# - 7 category : intergenic|exonic|intronic|encompassing(also known as overlapping)

# - 8 GeneId_Cod.Pot : Coding potential score computed by the GeneId software

# - 9 Genc_polyA : 0|1 : does the transcript have a polyA signal annotated by GENCODE in 100bp around TTS (1=yes/0=no)

# - 10 DiTAG_support : 0|1 : does the transcript have diTAG support for both ends (1=yes/0=no)

# - 11 5p_completeness_by_cage : 5' completeness based on 12 cell lines polyA+ whole cell cage data (cage clusters filtered by IDR 0.01 and TSS prediction strength >= 0.5) (1=yes/0=no).

# - 12 overV7Coding,overV3cCoding,overRefSeqCoding : 1|0 does the transcript have at least one exon overlapping (by at least 1 bp) in sense a protein coding exon of the 3 following datasets : gencode V7 protein coding exons, gencode V3c protein coding exons, RefSeq protein coding exons? (1=yes/0=no)

# - 13 overV7Coding,overV3cCoding,overRefSeqCoding : 0|1 => does the transcript overlap a protein-coding exon on the same strand? (1=yes/0=no)

# - 14 phastcons_primate_transcript_score : cumulative conservation score based on phastCons program at the transcript level in primate.

# - 15 phastcons_primate_intron_score : cumulative conservation score based on phastCons program at the intron level in primate.

# - 16 phastcons_primate_promoter_score : cumulative conservation score based on phastCons program at the promoter level in primate.

# - 17 phastcons_mammal_transcript_score : cumulative conservation score based on phastCons program at the transcript level in mammal.

# - 18 phastcons_mammal_intron_score : cumulative conservation score based on phastCons program at the intron level in mammal.

# - 19 phastcons_mammal_promoter_score : cumulative conservation score based on phastCons program at the promoter level in mammal.

# - 20 phastcons_vertebrate_transcript_score : cumulative conservation score based on phastCons program at the transcript level in vertebrate.

# - 21 phastcons_vertebrate_intron_score : cumulative conservation score based on phastCons program at the intron level in vertebrate.

# - 22 phastcons_vertebrate_promoter_score : cumulative conservation score based on phastCons program at the promoter level in vertebrate

# - 23 PrimatesSpe : 0|1 => is the transcript only found in primates? (1=yes/0=no)

# - 24 Human_1PrimateSpe : 0|1 => is the transcript only found in human + 1 primate species? (1=yes/0=no)

# - 25 Species_Homologs : list of species where putative lncRNA orthologue could be found (comma separated).

# - 26 gene_biotype : gene biotype as annotated in the source lncRNA gencode file.

# - 27 tx_biotype : transcript biotype as annotated in the source lncRNA gencode file.

# - 28 CSHL_WholeCell_LPA+-_15CellLines : format cellline1@RPKM1,cellline2@RPKM2... => RPKM at the gene level of the CELL compartment from the 115 CSHL RNASeq experiments (15 cell lines) where polyA+ and - together with bioreplicates were averaged.

# - 29 familyIndex : Name of the family.

# - 30 familySize : Size of the family (0 if no family).

# - 31 familyIndex_ARfiltered : Name of the family filtered for Repeats.

# - 32 familySize_ARfiltered : Size of the family filtered for Repeats (0 if no family).

Subclassifications of lncRNAs

The following files contain lists and classifications of lncRNAs as described in Derrien et al Figure 1B.

Files contain lncRNA coordinates in either in BED format, or in BEDPE format. For the latter, the coordinates and identity of the nearest protein coding gene are also provided.

Numbers indicate transcript counts.