Non-coding RNA lincRNA RNA-Seq Track Settings
 
lincRNA RNA-Seq reads expression abundances

Track collection: RNA sequences that do not code for a protein

+  Description
+  All tracks in this collection (4)

Maximum display mode:       Reset to defaults   

Show only items with score at or above:   (range: 0 to 1000)

Select views (Help):
RefSeq Expression Ratio ▾      
Select subtracks by tissue type:
Tissue Type
Adipose
Adrenal
Brain
Brain R
Breast
Colon
Foreskin R
Heart
hLF r1
hLF r2
Kidney
Liver
Lung
LymphNode
Ovary
Placenta R
Prostate
SkeletalMuscle
Testes
Testes R
Thyroid
WhiteBloodCell
Tissue Type
List subtracks: only selected/visible    all    ()
  views↓1 Tissue Type↓2   Track Name↓3  
 
dense
 Configure
 RefSeq Expression Ratio  Adipose  lincRNAs from adipose   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Adrenal  lincRNAs from adrenal   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Brain  lincRNAs from brain   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Brain R  lincRNAs from brain_r   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Breast  lincRNAs from breast   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Colon  lincRNAs from colon   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Foreskin R  lincRNAs from foreskin_r   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Heart  lincRNAs from heart   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  hLF r1  lincRNAs from hlf_r1   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  hLF r2  lincRNAs from hlf_r2   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Kidney  lincRNAs from kidney   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Liver  lincRNAs from liver   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Lung  lincRNAs from lung   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  LymphNode  lincRNAs from lymphnode   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Ovary  lincRNAs from ovary   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Placenta R  lincRNAs from placenta_r   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Prostate  lincRNAs from prostate   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  SkeletalMuscle  lincRNAs from skeletalmuscle   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Testes  lincRNAs from testes   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Testes R  lincRNAs from testes_r   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  Thyroid  lincRNAs from thyroid   Schema 
 
dense
 Configure
 RefSeq Expression Ratio  WhiteBloodCell  lincRNAs from whitebloodcell   Schema 
    
Data coordinates converted via liftOver from: Feb. 2009 (GRCh37/hg19)


Note: lifted from hg19

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