Evidence map›Paper›PMID 31117939›Full record

ArticleBMC genomics2019

EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins.

Pritha Ghosh, Adwait Joshi, Niang Guita, Bernard Offmann, R Sowdhamini

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

Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.2field-weighted citation impact, top 48% 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

2 citing papers in PubMed, 2 citations in OpenAlex.

  1. Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022
    Review
  2. 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

5 authors at 2 institutions in 3 countries.

Pritha GhoshNational Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, 560 065, India.
Adwait JoshiNational Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, 560 065, India.
Niang GuitaFaculty of Science and Technology, University of Nantes, Rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France.
Bernard OffmannFaculty of Science and Technology, University of Nantes, Rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France.
R SowdhaminiNational Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, 560 065, India. mini@ncbs.res.in.ORCID http://orcid.org/0000-0002-6642-2367
Tata Institute of Fundamental Research · INNantes Université · FR

Funding

JC Bose fellowship, Department of Science and Technology SB/S2/JCB-071/2015
6 · The paper itself

Abstract

The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism into a comprehensive database named EcRBPome. It contains RBPs recorded from 614 complete E. coli proteomes available in the RefSeq database (as of October 2018). The database provides various features related to the E. coli RBPs, like their domain architectures, PDB structures, GO and EC annotations etc. It provides the assembly, bioproject and biosample details of each strain, as well as cross-strain comparison of occurrences of various RNA-binding domains (RBDs). The percentage of RBPs, the abundance of the various RBDs harboured by each strain have been graphically represented in this database and available alongside other files for user download. To the best of our knowledge, this is the first database of its kind and we hope that it will be of great use to the biological community.

Indexed as

Databases, FactualComputational BiologyEscherichia coliEscherichia coli ProteinsProteomeRNA, BacterialRNA-Binding ProteinsEscherichia coli ProteinsProteomeRNA, BacterialRNA-Binding ProteinsCross-genome comparisonDatabaseEscherichia coliGenome-wide surveyPathotypesProteomesRNA-binding proteins

Identifiers

PMID31117939
PMCPMC6530084
OpenAlexW2953347063

What Socratic 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 Socratic graph.