Evidence map›Paper›PMID 20587619›Full record

ArticleRNA (New York, N.Y.)2010

Genome-wide computational identification and manual annotation of human long noncoding RNA genes.

Hui Jia, Maureen Osak, Gireesh K Bogu, Lawrence W Stanton, Rory Johnson, Leonard Lipovich

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 212 papers.

0numbers the graph read from it
0cells of the map it votes in
212citing papers in PubMed
8.6field-weighted citation impact, top 2% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

212 citing papers in PubMed, 394 citations in OpenAlex.

  1. Article
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  13. LncRNA MAFG-AS1 is involved in human cancer progression.European journal of medical research · 2023
    Review
  14. Article
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152 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 3 institutions in 2 countries.

Hui JiaCenter for Molecular Medicine and Genetics, Wayne State University, Detroit, MO 48202, USA.
Maureen Osak
Gireesh K Bogu
Lawrence W Stanton
Rory Johnson
Leonard Lipovich
Genome Institute of Singapore · SGWayne State University · USHillsdale College · US

Funding

Differential Expression and Regulatory Functions of Long Non-Coding RNA MoleculesR03DA026021 · NIDA · WAYNE STATE UNIVERSITY · PI LIPOVICH, LEONARD · 2008 to 2009
$301k
NIDA NIH HHS R03 1R03DA026021-01NIDA NIH HHS R03 DA026021
6 · The paper itself

Abstract

Experimental evidence suggests that half or more of the mammalian transcriptome consists of noncoding RNA. Noncoding RNAs are divided into short noncoding RNAs (including microRNAs) and long noncoding RNAs (lncRNAs). We defined complementary DNAs (cDNAs) lacking any positive-strand open reading frames (ORFs) longer than 30 amino acids, as well as cDNAs lacking any evidence of interspecies conservation of their longer-than-30-amino acid ORFs, as noncoding. We have identified 5446 lncRNA genes in the human genome from approximately 24,000 full-length cDNAs, using our new ORF-prediction pipeline. We combined them nonredundantly with lncRNAs from four published sources to derive 6736 lncRNA genes. In an effort to distinguish standalone and antisense lncRNA genes from database artifacts, we stratified our catalog of lncRNAs according to the distance between each lncRNA gene candidate and its nearest known protein-coding gene. We concurrently examined the protein-coding capacity of known genes overlapping with lncRNAs. Remarkably, 62% of known genes with "hypothetical protein" names actually lacked protein-coding capacity. This study has greatly expanded the known human lncRNA catalog, increased its accuracy through manual annotation of cDNA-to-genome alignments, and revealed that a large set of hypothetical-protein genes in GenBank lacks protein-coding capacity. In addition, we have developed, independently of existing NCBI tools, command-line programs with high-throughput ORF-finding and BLASTP-parsing functionality, suitable for future automated assessments of protein-coding capacity of novel transcripts.

Indexed as

Genome, HumanDatabases, Nucleic AcidDNA, ComplementaryGene Expression ProfilingGenomeHumansOpen Reading FramesProteinsRNA, UntranslatedDNA, ComplementaryProteinsRNA, Untranslated

Identifiers

PMID20587619
PMCPMC2905748
OpenAlexW2110356447

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.