Evidence map›Paper›PMID 26980280›Full record

ArticleNucleic acids research2016

f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome.

Shaojun Tang, Martin Hemberg, Ertugrul Cansizoglu, Stephane Belin, Kenneth Kosik, Gabriel Kreiman, Hanno Steen, Judith Steen

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

8 authors.

Shaojun TangDepartments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Martin HembergDepartment of Ophthalmology, Boston Children's Hospital, Boston, MA 02115, USA.
Ertugrul CansizogluF.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.
Stephane BelinF.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.
Kenneth KosikNeuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106, USA.
Gabriel KreimanDepartment of Ophthalmology, Boston Children's Hospital, Boston, MA 02115, USA.
Hanno SteenDepartments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA Hanno.Steen@Childrens.Harvard.edu.
Judith SteenF.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA Judith.Steen@Childrens.Harvard.edu.

Funding

Proteogenomics to characterize novel non-coding and extragenic translationR01GM112007 · NIGMS · BOSTON CHILDREN'S HOSPITAL · PI KREIMAN, GABRIEL, STEEN, JUDITH A · 2015 to 2018
$2.4M
Regulation of SMN and Identification of its Downstream TargetR01NS066973 · NINDS · BOSTON CHILDREN'S HOSPITAL · PI STEEN, JUDITH A · 2010 to 2014
$2.2M
NIGMS NIH HHS R01 GM112007NINDS NIH HHS R01 NS066973
6 · The paper itself

Abstract

The ability to integrate 'omics' (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different 'omics' data types or multi-dimensional data including time courses. We present fCI (f-divergence Cut-out Index), a model capable of simultaneously identifying DEGs from continuous and discrete transcriptomic, proteomic and integrated proteogenomic data. We show that fCI can be used across multiple diverse sets of data and can unambiguously find genes that show functional modulation, developmental changes or misregulation. Applying fCI to several proteogenomics datasets, we identified a number of important genes that showed distinctive regulation patterns. The package fCI is available at R Bioconductor and http://software.steenlab.org/fCI/.

Indexed as

Gene ExpressionAlgorithmsComputational BiologyGene Expression ProfilingProteomicsSequence Analysis, RNATandem Mass Spectrometry

Identifiers

PMID26980280
PMCPMC4889934

What OpenQuestion holds

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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.