NDLI: Computational Selection of Transcriptomics Experiments Improves Guilt-by-Association Analyses

Content Provider	PubMed Central
Author	Bhat, Prajwal Yang, Haixuan László, Bögre Devoto, Alessandra Alberto, Paccanaro
Editor	James, Provart Nicholas
Copyright Year	2012
Abstract	The Guilt-by-Association (GBA) principle, according to which genes with similar expression profiles are functionally associated, is widely applied for functional analyses using large heterogeneous collections of transcriptomics data. However, the use of such large collections could hamper GBA functional analysis for genes whose expression is condition specific. In these cases a smaller set of condition related experiments should instead be used, but identifying such functionally relevant experiments from large collections based on literature knowledge alone is an impractical task. We begin this paper by analyzing, both from a mathematical and a biological point of view, why only condition specific experiments should be used in GBA functional analysis. We are able to show that this phenomenon is independent of the functional categorization scheme and of the organisms being analyzed. We then present a semi-supervised algorithm that can select functionally relevant experiments from large collections of transcriptomics experiments. Our algorithm is able to select experiments relevant to a given GO term, MIPS FunCat term or even KEGG pathways. We extensively test our algorithm on large dataset collections for yeast and Arabidopsis. We demonstrate that: using the selected experiments there is a statistically significant improvement in correlation between genes in the functional category of interest; the selected experiments improve GBA-based gene function prediction; the effectiveness of the selected experiments increases with annotation specificity; our algorithm can be successfully applied to GBA-based pathway reconstruction. Importantly, the set of experiments selected by the algorithm reflects the existing literature knowledge about the experiments. [A MATLAB implementation of the algorithm and all the data used in this paper can be downloaded from the paper website: http://www.paccanarolab.org/papers/CorrGene/].
Related Links	http://dx.doi.org/10.1371/journal.pone.0039681
Starting Page	39681
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	8
Volume Number	7
Language	English
Publisher	Public Library of Science
Publisher Date	2012-08-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

Automated Masking of AFLP Markers Improves Reliability of Phylogenetic Analyses

Analyses and Comparison of Imputation-Based Association Methods

Fluctuating Selection Models and Mcdonald-Kreitman Type Analyses

Slim by Design: Serving Healthy Foods First in Buffet Lines Improves Overall Meal Selection

Heterogeneity in Meta-Analyses of Genome-Wide Association Investigations

Glioma Association and Balancing Selection of ZFPM2

Association and Mutation Analyses of 16p11.2 Autism Candidate Genes

Selection of Reliable Biomarkers from PCR Array Analyses Using Relative Distance Computational Model: Methodology and Proof-of-Concept Study

Computational Selection of Transcriptomics Experiments Improves Guilt-by-Association Analyses

Similar Documents

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

Automated Masking of AFLP Markers Improves Reliability of Phylogenetic Analyses

Analyses and Comparison of Imputation-Based Association Methods

Fluctuating Selection Models and Mcdonald-Kreitman Type Analyses

Slim by Design: Serving Healthy Foods First in Buffet Lines Improves Overall Meal Selection

Heterogeneity in Meta-Analyses of Genome-Wide Association Investigations

Glioma Association and Balancing Selection of ZFPM2

Association and Mutation Analyses of 16p11.2 Autism Candidate Genes

Selection of Reliable Biomarkers from PCR Array Analyses Using Relative Distance Computational Model: Methodology and Proof-of-Concept Study

Computational Selection of Transcriptomics Experiments Improves Guilt-by-Association Analyses