Evidence map›Paper›PMID 31372646›Full record

ArticleNucleic acids research2019

Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA).

Katherine A Pillman, Kaitlin G Scheer, Emily Hackett-Jones, Klay Saunders, Andrew G Bert, John Toubia, Holly J Whitfield, Sunil Sapkota, Laura Sourdin, Hoang Pham and 6 more

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

Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
0.6field-weighted citation impact, top 38% 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

10 citing papers in PubMed, 12 citations in OpenAlex.

  1. Article
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  5. Article
  6. Review
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  9. Review
  10. Illuminating lncRNA Function Through Target Prediction.Methods in molecular biology (Clifton, N.J.) · 2021
    Article
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

16 authors at 4 institutions in 1 country.

Katherine A PillmanCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Kaitlin G ScheerCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Emily Hackett-JonesCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Klay SaundersCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Andrew G BertCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
John ToubiaCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Holly J WhitfieldBioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
Sunil SapkotaCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Laura SourdinCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Hoang PhamSchool of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.
Thuc D LeSchool of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.
Joseph CursonsSchool of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.
Melissa J DavisSchool of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.
Philip A GregoryCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Gregory J GoodallCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
Cameron P BrackenCentre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.
South Australia Pathology · AUThe University of Melbourne · AUUniversity of South Australia · AUWalter and Eliza Hall Institute of Medical Research · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Epithelial-mesenchymal transition (EMT) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. Although EMT-regulatory roles for numerous miRNAs and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct miRNA targets from complex datasets and in deciding how to incorporate 'indirect' miRNA effects that may, or may not, represent biologically relevant information. To better understand how miRNAs exert effects throughout the transcriptome during EMT, we employed Exon-Intron Split Analysis (EISA), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of RNA-Seq reads mapping to exons and introns. We find that in response to the manipulation of miRNAs, a major effect on gene expression is transcriptional. We also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both EMT and mesenchymal to epithelial transition (MET) in response to TGF-β or miR-200c respectively. The prominent transcriptional influence of miRNAs was also observed in other datasets where miRNA levels were perturbed. This work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of EISA to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms.

Indexed as

Gene Regulatory NetworksRNA Processing, Post-TranscriptionalTranscription, GeneticCell LineComputational BiologyDatasets as TopicEpidermal Growth FactorEpithelial CellsEpithelial-Mesenchymal TransitionErbB ReceptorsExonsExtracellular Signal-Regulated MAP KinasesHumansIntronsMicroRNAsProto-Oncogene Proteins c-aktEGFR protein, humanEpidermal Growth FactorErbB ReceptorsExtracellular Signal-Regulated MAP KinasesMicroRNAsMIRN200 microRNA, humanProto-Oncogene Proteins c-aktRNA, MessengerTransforming Growth Factor beta

Identifiers

PMID31372646
PMCPMC6895270
OpenAlexW2965700171

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.