January 14, 2010

EGAN – Exploratory Gene Association Networks

Filed under: Bioinformatics,Systems Biology — Biointelligence: Education,Training & Consultancy Services @ 7:27 am
Tags: , , , ,

EGAN (Exploratory Gene Association Networks) is a software tool that allows a domain expert (a biologist) to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of entities (genes), relationships (protein-protein interactions, literature co-occurence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined entity subsets (gene lists), and provides direct links to web resources and literature (NCBI Entrez
Gene, PubMed, KEGG, Google, etc.).

EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio.

For more reading refer this link –

January 13, 2010

Database of human Protein-DNA Interactions – hPDI

Filed under: Bioinformatics,Computational Biology,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 6:05 am
Tags: , , , ,

The characterization of the protein-DNA interactions usually requires three levels of analysis:

1.Genetic: Determination of the nucleotide sequence of the protein-binding region and the identification of sequence changes that confer a mutated phenotype.

2. Biochemical: Identification of potential protein-DNA contacts using a variety of footprinting and protection experiments such as DNaseI or hydroxyl radical footprinting, and methylation protection or ethylation protection experiments.

3. Physical: Analysis of specific interactions in protein-target sequence fragment co-crystals.

The hPDI database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The current release of hPDI contains 17,718 protein-DNA interactions for 1013 human DNA-binding proteins. These DNA-binding proteins include 493 human transcription factors (TFs) and 520 unconventional DNA binding proteins (uDBPs). This database is freely accessible for any academic purposes.

hPDI can be accessed from here:

January 12, 2010

Comparative Genetic Maps visualisation: CMap3D

Filed under: Bioinformatics,Computational Biology — Biointelligence: Education,Training & Consultancy Services @ 5:52 am
Tags: , , , ,

Chromosome mapping by counting the number of recombinants produces a genetic map of the chromosome. But all the genes on the chromosome are incorporated in a single molecule of DNA. Genes are simply portions of the molecule (open reading frames or ORFs) encoding products that create the observed trait (phenotype). The rapid progress in DNA sequencing has produced complete genomes for hundreds of microbes and several eukaryotes.

Genetic linkage mapping enables the study of genome organisation and the association of heritable traits with regions of sequenced genomes and underlying genome sequence variation. Comparative genetic mapping is particularly powerful as it allows a translation of information between related genomes and gives an insight into genome evolution.

CMap3D isĀ  powerful tool to graphically compare multiple genetic maps in three-dimensional space.CMap3D is a stand-alone application and is available for Windows, OS X, and Linux. This software is free for academic users.

For more information refer this link: