mxplore: miRNA-gene interactions

Processed files for mxplore.

Files needed for running mxplore:

The mxplore_required_data.zip archive contains:

exclude files for text mining (e.g. ambiguous names) (excludes)

input ontology files in obo-format (obodir)

output synonym lists used for text mining (synonyms)

files required for mapping NCIT gene identifiers to symbols ( ncit_conversion_folder )

The archive is to be unzipped within the mxplore main folder and to be named required_data.

Front-end files:

IGV.js compatible gene definitions:

Organism/genome
Type
Filename

mouse/mm10
gene
mm10_gene_annotation.pickle

mouse/mm10
miRNA
mm10_mirna_annotation.pickle

human/hg19
gene
hg19_gene_annotation.pickle

human/hg19
miRNA
hg19_mirna_annotation.pickle

sqlite database including context information for all relevant interaction documents: cons_evidences.db

miRNA-gene interactions (without context information) for all mxplore interactions: mxplore_table_mx.tsv

For source code, please visit the project GitHub at https://github.com/mjoppich/mxplore .

Intermediate Output Files

The aggregated_results.zip contain all aggregated miRNA-gene interactions as well as context information after running createEntEntRelation.py and createContextInfo.py .