HRBC Genomics Network Software Area: Analysis Tools

ISA/CNR Gene Expression Analysis Tool

ISA/CNR new tool for visualization and analysis of gene expression data.

ISA/CNR Protein Tools

Includes:

DBSCAN

a tool to search for sequence patterns within protein and nucleic acid databases (currently accessible only to local users).

NUCSCAN

a tool to search for sequence pattern within a single nucleic acid sequence (currently accessible only to local users).

PROSCAN

a tool to search for sequence pattern within a single protein, and to analyze amino acid composition.

HELM

searching for helix motifs.

Web-ACF

Web Analyzer of Conformational Features, based on the 3D protein structure (currently accessible only to group users).

MedMole

Mining On-Line Expert on MedLine - A text mining on-line service. MedMOLE searches into Medline abstracts, retrieves relevant documents and performs text mining analysis. The aim is to improve the comprehension of microarray experimental results by grouping co-regulated genes on the basis of MEDLINE documents.

GOAL - Gene Ontology Automated Lexicon

From the documentation:
This scripts performs statistical analysis of Gene ontology terms from an Eisen formatted expression table, after performing a t score analysis.
The first column contains the EST id (CloneID or Genbank Accession number). The application perform a t test analysis. The t score is then associated to each EST, together to its Unigene Cluster and averaged if different EST belonging to the same Unigene cluster are present. Then it retrieves the GO terms associated to each Unigene Cluster and it computes the average score for each GO term. A bootstrap is performed by permutating GO terms and ESTs and a frequency distribution is obtained in order to generate p-values relative to the GO term scores.
Since the two samples groups in the expression table might be very different in the expression profiles, to reduce bias towards the bootstrapping procedure, a number of t score from balanced permutations of the two groups in the expression tables are used for the bootstrapi of GO terms.

AMARGE (IST mirror, authors: S. Kalko, IDIBAPS, J. Lozano, CRG, Barcelona)

QC analysis and calculation of Affy chips expression values using RMA from a zip.
Submit your .cel files (up to 50) and retrieve:

• Raw density data graph
• RNA digestion plot
• Graphical representation of every chip
• Boxplot of Nomalized unscaled standard error
• Boxplot of relative log expressions
• RMA expression tables
• Annotation table