microRNA target information

Name Description Date accessed Ref
miRTarBase Experimentally supported microRNA target interactions. May 2016 (v6.1)
miRecords Experimentally supported microRNA target interactions. May 2016 (v5.0)
DIANA microT-CDS Predicted microRNA target interactions. May 2016
ElMMo3 Predicted microRNA target interactions. May 2016 (v3)
MicroCosm Predicted microRNA target interactions. May 2016 (v5)
microRNA.org Predicted microRNA target interactions. May 2016
miRDB Predicted microRNA target interactions. May 2016 (v5)
miRNAMap2 Predicted microRNA target interactions. May 2016
PicTar2 Predicted microRNA target interactions. May 2016 (v2)
PITA Predicted microRNA target interactions. May 2016 (v6)
TargetScanMouse Predicted microRNA target interactions. May 2016 (v7.1)

lncRNA target information

Name Description Date accessed Ref
LncRNADisease Experimentally supported lncRNA target interactions. May 2016
LncRNA2Target Experimentally supported lncRNA target interactions. May 2016 (v1.2)
LncReg Experimentally supported lncRNA target interactions. May 2016

piRNA target information

Name Description Date accessed Ref
piRBase Experimentally supported piRNA target interactions. May 2016 (v1.0)

Immunological gene information

Name Description Date accessed Ref
InnateDB InnateDB contains mouse genes that play role in immunological processes mined from literature. This collection of genes, together with the SepticShock genes (see below), are the core of the mouse immunological gene set. All human genes were converted to mouse via NCBI Homologene. May 2016
SepticShock Contains mouse genes that play role in immunological processes. The list includes genes with potential relevance to macrophage response to microbial stimulation. May 2016
ImmPort The list of immunologically related genes in ImmPort is a collection of human genes, which was formed with the goal of retrieving all genes that have immune system-related functions. All human genes were converted to mouse via NCBI Homologene. May 2016
Immunome database Immunology-related human genes were collected from research articles, textbooks and electronic information sources. The list contains genes that are directly involved in immunological processes. All human genes were converted to mouse via NCBI Homologene. May 2016
Immunogenetic Related Information Source This gene list, of human immune genes (April 28, 2013), is derived from the IRIS online database of known defence genes (note that the IRIS database does not seem to be available anymore). All human genes were converted to mouse via NCBI Homologene. May 2016
MAPK/NFKB network This human gene list was derived from in house curation of the p38, ERK, JNK signalling pathways (Raymond Lo and Fiona Roche) and the NFKB transcriptional regulatory module (Jenn Gardy). It contains 761 genes (April 28, 2013); members of the TNF-alpha and IFN-alpha signalling pathway derived from Transpath data were also included. All human genes were converted to mouse via NCBI Homologene. May 2016

General

Name Description Date accessed Ref
miRBase General information about microRNA. May 2016 (v21)
NCBI gene General information about target genes. Feb 2016
Wikipathways Wikipathways information for target genes. Jun 2016
KEGG: Kyoto Encyclopedia of Genes and Genomes Pathway information for target genes. Feb 2014
REACTOME REACTOME pathway information for target genes. Jun 2016
Gene Ontology Biological processes and biological functions associated to target genes. Feb 2016
MSigDB Information about human target gene differential expression in immunological experiments. The data is derived from multiple species and converted in MSigDB to human. All human genes were converted to mouse via NCBI Homologene. Jan 2016 (v5.1)
Cell-type expression Information on cell-types expressing miRNAs 2016
TFBS: Encode ChIP-based TFBS. Mapped to mm10 as described in the manuscript. 2016
TFBS: htChIP ChIP-based TFBSs. Mapped to mm10 as described in the manuscript. 2016