GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.

Avigail Taylor, Julia Steinberg, Tallulah S Andrews, Caleb Webber

Open access · hybridAbstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it

0cells of the map it votes in

6citing papers in PubMed, 1 pooled it

1.1field-weighted citation impact, top 22% 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

6 citing papers in PubMed, 1 synthesis or guideline pooled it, 16 citations in OpenAlex.

A Comprehensive Analysis of Nuclear-Encoded Mitochondrial Genes in Schizophrenia.Biological psychiatry · 2018
Pooled it
Identification of Prognostic Metabolomic Biomarkers at the Interface of Mortality and Morbidity in Pre-Existing TB Cases Infected With SARS-CoV-2.Frontiers in cellular and infection microbiology · 2022
Article
Fasting-induced FOXO4 blunts human CD4Nature metabolism · 2021
Article
A Proteomic Network Approach across the Kidney Stone Disease Reveals Endoplasmic Reticulum Stress and Crystal-Cell Interaction in the Kidney.Oxidative medicine and cellular longevity · 2019
Article
IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study.PLoS medicine · 2016
Article
Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways.Translational psychiatry · 2016
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

4 authors at 3 institutions in 1 country.

Avigail TaylorMRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

Julia SteinbergMRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

Tallulah S AndrewsMRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

Caleb WebberMRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

Genomics (United Kingdom) · GBCentre for Human Genetics · GBUniversity of Oxford · GB

Funding

Medical Research Council MC_UP_A320_1004Medical Research Council MC_UU_12021/4Wellcome Trust 090532/Z/09/ZWellcome Trust 093941/Z/10/Z

6 · The paper itself

Abstract

summaryWe present GeneNet Toolbox for MATLAB (also available as a set of standalone applications for Linux). The toolbox, available as command-line or with a graphical user interface, enables biologists to assess connectivity among a set of genes of interest ('seed-genes') within a biological network of their choosing. Two methods are implemented for calculating the significance of connectivity among seed-genes: 'seed randomization' and 'network permutation'. Options include restricting analyses to a specified subnetwork of the primary biological network, and calculating connectivity from the seed-genes to a second set of interesting genes. Pre-analysis tools help the user choose the best connectivity-analysis algorithm for their network. The toolbox also enables visualization of the connections among seed-genes. GeneNet Toolbox functions execute in reasonable time for very large networks (∼10 million edges) on a desktop computer. AVAILABILITY AND IMPLEMENTATION: GeneNet Toolbox is open source and freely available from http://avigailtaylor.github.io/gntat14. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: avigail.taylor@dpag.ox.ac.uk.

Indexed as

AlgorithmsDatabases, GeneticGene Regulatory NetworksSoftwareComputational BiologyComputer GraphicsGene Expression RegulationHumansInformation Storage and RetrievalMetabolic Networks and PathwaysSequence Analysis, DNAUser-Computer Interface

Identifiers

PMID25319962

DOI10.1093/bioinformatics/btu669

PMCPMC4308667

OpenAlexW2168951863

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.