Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) Datasets
Julie Dickerson
Gaurav Kandoi
10.25380/iastate.7218602.v2
https://iastate.figshare.com/articles/dataset/Tissue-spEcific_mrNa_iSoform_functIOnal_Networks_TENSION_Datasets/7218602
This folder contains the datasets used to build Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) and the 17 tissue-specific mRNA isoform level functional networks. README file contains descriptions for each of the files.<div><br></div><div>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.</div><div><br></div><div><b>Version 2:</b> improvements were made to the framework resulting in better performance and new datasets.<br></div>
2019-01-09 15:36:48
Alternative Splicing
mRNA Isoform Networks
Tissue-specific,
mouse
Random Forests
Biological Networks
Machine Learning
TENSION
Transcript-level Networks
Gene Ontology
network prediction
Functional Networks
sequence features
RNA-Seq
Tissue expression profile
Bioinformatics
Genetics
Genomics
Computational Biology
Molecular Biology
Gene Expression (incl. Microarray and other genome-wide approaches)
Proteins and Peptides
Animal Cell and Molecular Biology
Animal Structure and Function
Genome Structure and Regulation
Proteomics and Intermolecular Interactions (excl. Medical Proteomics)
Quantitative Genetics (incl. Disease and Trait Mapping Genetics)