Comparative Co-Expression Network Construction and Visualization.
CoExpNetViz takes as input a set of bait genes chosen by you and at least one pre-processed gene expression dataset. You can also specify a negative and positive cutoff value, which will be used to determine if two genes are co-expressed or not.
CyClus3D is a Cytoscape plugin for identifying functional modules in integrated networks composed of multiple interaction types. CyClus3D operates by clustering user-defined 3-node network motifs.
We present an ontology-driven framework to infer and visualise an arbitrary set of condition-specific responses against a reference network. To this end, we have implemented algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardized methodology that allows a unified view on differential networks and promotes comparability between differential network studies.
EP3 is a tool for the identification of the core region of a eukaryotic gene promoter. It uses universal properties of the promoter to detect those regions in a whole genome context. EP3 has been tested on several eukaryotes ranging from protists to human. On human it is, at the moment, the best performing tool to identify regions that are associated with transcription initiation.
EuGene is a gene prediction software for eukaryotic organisms. It is currently mainly tuned for plant and fungal genomes.
To use EuGene, paste/upload the sequence to analyze in the first table below. The size of the genomic sequence to be annotated is limited to3 Mb. If you provide a multifasta file it must have less than 400 sequences.
EVEX is a large-scale text mining resource containing millions of biomolecular events extracted from PubMed abstracts and PubMed Central full-text articles. The data in EVEX can be accessed by pubmed ID, gene/protein symbol, Entrez Gene ID, UniProt ID or through gene families. This rich resource is distributed as a MySQL database, can be browsed via an online web application, and is accessible through an API.
GenomeView is a stand-alone sequence browser specifically designed to visualize and manipulate a multitude of genomics data interactively.
hfAIM: a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms
Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements – the presence of acidic amino acids and the absence of positively charged amino acids in certain positions - to reliably identify AIMs in proteins.
