Evidence map›Paper›PMID 25060758›Full record

ArticleMolecular & cellular proteomics : MCP2014

Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

Dhanashree S Kelkar, Elayne Provost, Raghothama Chaerkady, Babylakshmi Muthusamy, Srikanth S Manda, Tejaswini Subbannayya, Lakshmi Dhevi N Selvan, Chieh-Huei Wang, Keshava K Datta, Sunghee Woo and 24 more

Open access · hybridAbstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular & cellular proteomics : MCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.

0numbers the graph read from it
0cells of the map it votes in
22citing papers in PubMed
3.6field-weighted citation impact, top 6% 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

22 citing papers in PubMed, 60 citations in OpenAlex.

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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

34 authors at 7 institutions in 2 countries.

Dhanashree S KelkarFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
Elayne Provost§Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205;
Raghothama Chaerkady¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
Babylakshmi MuthusamyFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India;
Srikanth S MandaFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
Tejaswini SubbannayyaFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
Lakshmi Dhevi N SelvanFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
Chieh-Huei Wang¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
Keshava K DattaFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡‡School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India;
Sunghee Woo§§Department of Computer Science, University of California, San Diego, California 92093;
Sutopa B DwivediFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
Santosh RenuseFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
Derese Getnet¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
Tai-Chung Huang¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
Min-Sik Kim¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
Sneha M PintoFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India;
Christopher J Mitchell¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
Anil K MadugunduFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
Praveen KumarFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
Jyoti SharmaFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India;
Jayshree AdvaniFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
Gourav DeyFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India;
Lavanya BalakrishnanFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖‖Department of Biotechnology, Kuvempu University, Shimoga 577 451, India;
Nazia SyedFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605 014, India;
Vishalakshi NanjappaFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
Yashwanth SubbannayyaFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
Renu GoelFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
T S Keshava PrasadFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India;
Vineet Bafna§§Department of Computer Science, University of California, San Diego, California 92093;
Ravi SirdeshmukhFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
Harsha GowdaFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
Charles WangThe Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350; pandey@jhmi.edu sleach1@jhmi.edu chwang@llu.edu.
Steven D Leach§Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; pandey@jhmi.edu sleach1@jhmi.edu chwang@llu.edu.
Akhilesh PandeyFrom the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 pandey@jhmi.edu sleach1@jhmi.edu chwang@llu.edu.
Institute of Bioinformatics · INAmrita Vishwa Vidyapeetham · INJohns Hopkins Medicine · USJohns Hopkins University · USManipal Academy of Higher Education · INUniversity of California, San Diego · USLoma Linda University · US

Funding

BIOCHEMISTRY, CELLULAR AND MOLECULAR BIOLOGY PROGRAMT32GM007445 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI GREEN, RACHEL · 1985 to 2021
$24.1M
Predoctoral Training Program in Human GeneticsT32GM007814 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 1985 to 2021
$10.6M
TrainingP41GM103484 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PEVZNER, PAVEL A · 2012 to 2018
$8.7M
NIGMS NIH HHS P41 GM103484NIGMS NIH HHS T32 GM007445NIGMS NIH HHS T32 GM007814Wellcome Trust
6 · The paper itself

Abstract

Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes.

Indexed as

Amino Acid SequenceAnimalsBase SequenceGene Expression ProfilingGenomeHigh-Throughput Nucleotide SequencingMass SpectrometryMolecular Sequence AnnotationProteomeProteomicsSequence Analysis, RNATranscriptomeZebrafishProteome

Identifiers

PMID25060758
PMCPMC4223501
OpenAlexW2160352483

What OpenQuestion holds

Textmetadata
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Registered trials

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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.