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Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) Collection

Version 4 2019-01-09, 15:39
Version 3 2018-10-29, 19:55
Version 2 2018-10-25, 21:15
Version 1 2018-10-23, 21:33
Posted on 2019-01-09 - 15:39 authored by Gaurav Kandoi
The files for this project have been split into three separate download packages:
- Predictions
- Scripts
- Datasets
Each package has a copy of the readme file which covers all three packages.

Alternative Splicing produces multiple mRNA isoforms of a gene which have important diverse roles such as regulation of gene expression, human heritable diseases, and response to environmental stresses. However, very little has been done to assign functions at the mRNA isoform level. Functional networks, where the interactions are quantified by their probability of being involved in the same biological process are typically generated at the gene level. We use a diverse array of tissue-specific RNA-seq datasets and sequence information to train random forest models for predicting the functional networks following a leave-one-tissue-out strategy. Since there is no mRNA isoform-level gold standard, we use single isoform genes co-annotated to Gene Ontology biological process annotations, Kyoto Encyclopedia of Genes and Genomes pathways, BioCyc pathways and protein-protein interactions as functionally related (positive pair). To generate the non-functional pairs (negative pair), we use the Gene Ontology annotations tagged with “NOT” qualifier. We describe 17 Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) in addition to an organism level reference functional network for mouse. We validate our predictions by comparing its performance with previous methods, randomized positive and negative class labels, updated Gene Ontology annotations, and by literature evidence.

Version 2: improvements were made to the framework resulting in better performance and new datasets.

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3 Biotech
3D Printing in Medicine
3D Research
3D-Printed Materials and Systems
4OR
AAPG Bulletin
AAPS Open
AAPS PharmSciTech
Abhandlungen aus dem Mathematischen Seminar der Universität Hamburg
ABI Technik (German)
Academic Medicine
Academic Pediatrics
Academic Psychiatry
Academic Questions
Academy of Management Discoveries
Academy of Management Journal
Academy of Management Learning and Education
Academy of Management Perspectives
Academy of Management Proceedings
Academy of Management Review
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FUNDING

ABI Innovation: Model-based Alternative Splicing Analysis Across Expression Platforms

Directorate for Biological Sciences

XSEDE 2.0: Integrating, Enabling and Enhancing National Cyberinfrastructure with Expanding Community Involvement

Directorate for Computer & Information Science & Engineering

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