NDLI: Success in the DREAM3 Signaling Response Challenge Using Simple Weighted-Average Imputation: Lessons for Community-Wide Experiments in Systems Biology

Content Provider	PubMed Central
Author	Clarke, Neil D. Bourque, Guillaume
Editor	Mark, Isalan
Abstract	Our group produced the best predictions overall in the DREAM3 signaling response challenge, being tops by a substantial margin in the cytokine sub-challenge and nearly tied for best in the phosphoprotein sub-challenge. We achieved this success using a simple interpolation strategy. For each combination of a stimulus and inhibitor for which predictions were required, we had noted there were six other datasets using the same stimulus (but different inhibitor treatments) and six other datasets using the same inhibitor (but different stimuli). Therefore, for each treatment combination for which values were to be predicted, we calculated rank correlations for the data that were in common between the treatment combination and each of the 12 related combinations. The data from the 12 related combinations were then used to calculate missing values, weighting the contributions from each experiment based on the rank correlation coefficients. The success of this simple method suggests that the missing data were largely over-determined by similarities in the treatments. We offer some thoughts on the current state and future development of DREAM that are based on our success in this challenge, our success in the earlier DREAM2 transcription factor target challenge, and our experience as the data provider for the gene expression challenge in DREAM3.
Related Links	http://dx.doi.org/10.1371/journal.pone.0008417
Starting Page	8417
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	1
Volume Number	5
Language	English
Publisher	Public Library of Science
Publisher Date	2010-01-26
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	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

A Top-Performing Algorithm for the DREAM3 Gene Expression Prediction Challenge

A Top-Performing Algorithm for the DREAM3 Gene Expression Prediction Challenge

Gene Expression Prediction by Soft Integration and the Elastic Net—Best Performance of the DREAM3 Gene Expression Challenge

Multiple Imputations Applied to the DREAM3 Phosphoproteomics Challenge: A Winning Strategy

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

Gene Expression Prediction by Soft Integration and the Elastic Net—Best Performance of the DREAM3 Gene Expression Challenge

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

Field experiments of success-breeds-success dynamics

Success in the DREAM3 Signaling Response Challenge Using Simple Weighted-Average Imputation: Lessons for Community-Wide Experiments in Systems Biology

Similar Documents

A Top-Performing Algorithm for the DREAM3 Gene Expression Prediction Challenge

A Top-Performing Algorithm for the DREAM3 Gene Expression Prediction Challenge

Gene Expression Prediction by Soft Integration and the Elastic Net—Best Performance of the DREAM3 Gene Expression Challenge

Multiple Imputations Applied to the DREAM3 Phosphoproteomics Challenge: A Winning Strategy

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

Gene Expression Prediction by Soft Integration and the Elastic Net—Best Performance of the DREAM3 Gene Expression Challenge

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

Field experiments of success-breeds-success dynamics

Success in the DREAM3 Signaling Response Challenge Using Simple Weighted-Average Imputation: Lessons for Community-Wide Experiments in Systems Biology