Evidence map›Paper›PMID 27934932›Full record

ArticleScientific reports2016

Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development.

Zhuo Wen, Geng Chen, Sibo Zhu, Jinhang Zhu, Bin Li, Yunjie Song, Suqing Li, Leming Shi, Yuanting Zheng, Menglong Li

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Article
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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

10 authors.

Zhuo WenCollege of Chemistry, Sichuan University, Chengdu 610064, China.
Geng ChenCenter for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
Sibo ZhuCenter for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
Jinhang ZhuCenter for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
Bin LiCenter for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
Yunjie SongCenter for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
Suqing LiCollege of Chemistry, Sichuan University, Chengdu 610064, China.
Leming ShiCenter for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
Yuanting ZhengCenter for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
Menglong LiCollege of Chemistry, Sichuan University, Chengdu 610064, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Accumulating evidence suggests that noncoding RNAs (ncRNAs) have important regulatory functions. However, lacking of functional annotations for ncRNAs hampered us from carrying out the subsequent functional or predictive research. Here we dissected the expression profiles of 3,458 rat noncoding genes using rat bodymap RNA-sequencing data consisting of 11 solid organs over four developmental stages (juvenile, adolescent, adult and aged) from both sexes, and conducted a comprehensive analysis of differentially expressed noncoding genes (DEnGs) between various conditions. We then constructed a co-expression network between protein-coding and noncoding genes to infer biological functions of noncoding genes. Modules of interest were linked to online databases including DAVID for functional annotation and pathway analysis. Our results indicated that noncoding genes are functionally enriched through pathways similar to those of protein-coding genes. Terms about development of the immune system were enriched with genes from age-related modules, whereas terms about sexual reproduction were enriched with genes in sex-related modules. We also built connection networks on some significant modules to visualize the interactions and regulatory relationship between protein-coding and noncoding genes. Our study could improve our understanding and facilitate a deeper investigation on organ/age/sex-related regulatory events of noncoding genes, which may lead to a superior preclinical model for drug development and translational medicine.

Indexed as

Gene Expression ProfilingGene Expression Regulation, DevelopmentalRNA, UntranslatedTranscriptomeAge FactorsAnimalsComputational BiologyFemaleGene Regulatory NetworksMaleMolecular Sequence AnnotationOrgan SpecificityRatsSex FactorsRNA, Untranslated

Identifiers

PMID27934932
PMCPMC5146941

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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.