List of links of interest to the HRBC Genomics Network project

Some useful web sites

• Mirror sites

GeneCards Mirror at CRISCEB

Bioconductor Mirror at the University of Ferrara

• Partners' sites

Bioinformatics at CINECA

Bioinformatics activities at CINECA, Bologna.





BioGate

Portal to Bioinformatics activities in Italy and the home for the FIRB-sponsored project "Bioinformatics for Genomics and Proteomics".





The Gene Expression Group Home Page

The Gene Expression Group at CRISCEB, Second University of Naples.





Functional Genomics Lab of the University of Ferrara

Analysis of Expression Profiles - by Use of cDNA microarrays
You can find here datasets and software relating to projects undertaken at the Functional Genomics Laboratory (PI: Dr Stefano Volinia)





• Sites of general interest

Microarray Informatics at the EBI

The microarray informatics group at the EBI addresses the problem(s) of managing, storing and analysing microarray data. Includes ArrayExpress, MIAMExpress, Expression Profiler, MGED (Microarray Gene Expression Data Society), SOFG (Standards and Ontologies for Functional Genomics).





GEO - Gene Expression Omnibus (NCBI)

The Gene Expression Omnibus is a high-throughput gene expression / molecular abundance data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval.





SMD - Stanford Microarray Database (Stanford University)

SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization. Data are released to the public at the researcher's discretion or upon publication





VIB MicroArray Facility

In April 1999, the Flanders Interuniversity Institute for Biotechnology (VIB) initiated a core facility for cDNA MicroArray analysis. The facility became operational in December 1999 and is located at Gasthuisberg, Leuven, Belgium. The purpose of the facility is to provide researchers access to a full MicroArray analysis service that includes:

• Dedicated Service Facility for MicroArray Analysis
• Advice in Experimental set-up
• Advice in choosing the appropriate technology platform
• Quality check of RNA integrity and purity
• Probe labeling starting from 5µg down to 100ng total RNA
• Quality check of labeled material
• Hybridisation, Scanning and Image Analysis
• Data pre-processing
• MicroArray follow-up with customized small size cDNA-arrays
• Advice in Data Analysis

The Facility supports 4 different MicroArray platforms:

• VIB In-House cDNA and Oligo-MicroArrays
• Affymetrix, GeneChip®
• Agilent Technologies, Agilent SurePrint
• Amersham Biosciences, CodeLink™





NCI Gene Expression Data Portal

The Gene Expression Data Portal (GEDP) hosts a variety of microarray experiments from geographically dispersed laboratories. Researchers can submit experiments for private or public view, retrieve publicly available experiments as well as the associated experiment files, and download experiment data in raw format or as XML documents based on the Microarray Gene Expression Markup Language (MAGE-ML). Researchers can also compare and analyze experiments via the XpressionWay tool which graphically illustrates the genes on the chip and the cellular pathways in which the genes operate.





CHIP - Children's Hospital Informatics Program

The Children's Hospital Informatics Program (CHIP) is a multidisciplinary applied research and education program at Children's Hospital in Boston. CHIP focuses on both bioinformatics and clinical informatics. The faculty is diverse, including physicians with additional training in information science and computer scientists with expertise in the biological sciences. CHIP encourages collaboration and provides shared resources to develop innovative information technologies with the goal of both enhancing biomedical research and improving patient care. CHIP also serves as the bioinformatics core for several national genomics investigations.
Software tools for gene expression analysis are available at http://www.chip.org/home/resources.cgi .





Gene Expression Analysis Workshop (GEAW)

From the home page:
The GEAW is being developed as part of The NCI Director's Challenge: Toward a Molecular Classification of Cancer, which challenges the scientific community to harness the power of comprehensive molecular analysis technologies to redefine tumor classification, moving from morphological to molecular classification.
The GEAW is modeled after the Genetic Analysis and Protein Structure Prediction Workshops, and is intended to aid the development of our analytic tools by providing challenge sets for analytic tool evaluation and assessment.
The purpose of this site is to facilitate the communication among individual groups addressing the challenge in analyzing data generated from the use of microarray technology.





Micro-Array Department (MAD) at the University of Amsterdam (UvA)

The Micro-Array Department (MAD) of the Institute for life Sciences (SILS) at the Faculty of Science (FNWI) from the University of Amsterdam (UvA) is a fully licensed micro-array technology center with spotted-array and Affymetrix Genechip® platforms, which operates as a service provider with collaborations and service contracts with academic research groups and industry. A group of 16 people working within the unit provide advice, services and support related to micro-array technology and appropriate bioinformatics for-profit and not-for-profit parties.





Tools for Analysis of DNA Microarray Data at the Center for Biological Sequence Analysis (CBS) at the Technical University of Denmark (DTU)

This site includes the following analysis tools:

• qspline for normalization of Affymetrix array data and spotted array data is now part of the affyR package.
• affyR package contains routines for handling Affymetrix array data.
• ClustArray for clustering array data.
• ProbeWiz for design of probes for spotted arrays.





GEDA - Gene Expression Data Analysis Tool at the University of Pittsburgh





Nuclear Receptors Resources Georgetown University

The Nuclear Receptor Resource (NRR) Project is a collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily.
The following components are included:

• Nuclear Receptor Resources (databases, tools, investigators, journals online, research funding, meetings, employments)
• NRR Components: Androgen Receptor (AR), Estrogen Receptor (ER), Glucocorticoid Receptor (GR), Peroxisome Proliferator-Activated Receptor (PPAR), Steroid Receptor Associated Proteins (SRAPR), Thyroid Receptor (TR), Vitamin D Receptor
• Related NRR links: Steroid Structures, Graphics Library





NURSA - Nuclear Receptor Signaling Atlas

From the site:

"The long term goal of this website is to harness of the power of the Internet for the benefit of the global nuclear receptor signaling community. Our strategy is to involve the members of this community as active contributors and reviewers to maintain the quality and immediacy of the content on the site.

To this end we are developing browser-based features to enhance and facilitate the interaction between the community and the NURSA web portal:
NURSA e-journal Forms for the submission of research data for publication
Laboratories Post and maintain your own laboratory page
Forum Share news & views, methods and protocols, and more
Jobs Post and browse opportunities in the field

We are excited at the prospect of developing these features and others for the community, and hope that you share our enthusiasm at what we as a community might with time achieve. The NURSA website will realize its full potential only with the support of you, the researcher, so we encourage you make full use of the feedback forms throughout the site to let us know what you think of our work so far, and how it might be improved.

Best wishes,
Neil McKenna






NucleaRDB home page





Nuclear Receptor (Journal) Home page