An online tool for identification of micorRNA-mediated module which is formed by protein-protein interactions (PPIs). Mirin integrates microRNA regulations and PPIs with microRNA/mRNA expression data to identify the perturbed microRNA regulatory modules and reveals their functional roles in specific biological conditions.
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Hosts a network-assisted hypothesis-generating server for C. elegans. WormNet includes a base gene network, which substantially improved predictions of RNAi phenotypes. The server generates various gene network-based hypotheses using three complementary network methods: (i) a phenotype-centric approach to ‘find new members for a pathway’; (ii) a gene-centric approach to ‘infer functions from network neighbors’ and (iii) a context-centric approach to ‘find context-associated hub genes’, which is a method to identify key genes that mediate physiology within a specific context.
Serves for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. SNMNMF is a program that presents the following characteristics: (1) integrates prior knowledge such as a gene interaction network as a constraint on the solution space; (2) allows users to upload several different types of data; (3) and provides sparse solutions. Moreover, this tool can be used for many problems involving heterogeneous data sources.
Detects synergistic miRNA regulatory modules. Mirsynergy operates in two stages: it first forms microRNA regulatory modules (MiRMs) based on co-occurring microRNA (miRNA) targets and then expands each MiRM by greedily including (excluding) mRNAs into (from) the MiRM to maximize the synergy score, which is a function of miRNA-mRNA and gene-gene interactions.
Allows measurement of pathway activity and crosstalk among pathways. StarBioTrek was developed for the identification of a network of dependent pathways and their regulatory miRNAs. It was used for revealing microRNA (miRNAs) that can regulate, in a coordinated way, networks of gene pathways and permitted to identify pairwise pathways for breast cancer (BC) subtypes able to discriminate BC versus normal samples.
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Discover our proposed protocols.
They are easy to use or edit to meet your needs.
They are easy to use or edit to meet your needs.
Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging
Tools (4):
TopGO, NAViGaTOR, WormNet, GEO
Topics (1):
RNA-seq analysis
Massively Parallel Sequencing and Analysis of the Necator americanus Transcriptome
Tools (12):
CAP3, BLASTX, BLASTN, Blast2GO, InterProScan, KOBAS, SignalP, TMHMM, BLASTP, WormNet, WormBase, KO
Topics (9):
RNA-seq analysis, Necator americanus, Caenorhabditis elegans, Homo sapiens, Canis lupus familiaris, Infection, Amino Acids, Calcium, Metals, Alkaline Earth