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COXPRESdb

http://coxpresdb.hgc.jp/

Description :
Coexpressed genes and networks in human and mouse

miRGator

http://genome.ewha.ac.kr/miRGator/miRGator.html

Description :
microRNA target prediction, functional analysis, and gene expression data

HEG-DB

http://genomes.urv.cat/HEG-DB

Description :
Predicted highly expressed genes in prokaryotic genomes

FlyEx

http://flyex.ams.sunysb.edu/flyex

Description :
FlyEx is a spatiotemporal atlas of segmentation gene expression. The important feature that sets FlyEx apart from other spatiotemporal atlases is the availability of highly accurate quantitative gene expression data. FlyEx supports operations on images of gene expression patterns and allows a user to monitor and analyze the dynamics of formation of segmentation gene expression domains over the whole period of segment determination, that amounts to 1.5 h of development.

Aknowledgement :
FlyEx development is supported by the National Institutes of Health (RR07801) and the Grant Assistant Program of the Civilian Research and Development Foundation (RUB1-1578-ST-05).

References :
1Poustelnikova, E., Pisarev, A., Blagov, M., Samsonova, M., and Reinitz, J. (2004). A database for management of gene expression data in situ. Bioinformatics, 20: 2212-2221.2Samsonova, M., Pisarev, A., and Blagov, M. (2003). Processing of natural language queries to a relational database. Bioinformatics, 19, Suppl. 1, i241-i249.

Sebida

http://www.sebida.de/

Description :
Sex bias in insect gene expression database

GEISHA

http://geisha.arizona.edu/

Description :
GEISHA (Gallus Expression In Situ Hybridization Analysis) is a centralized and comprehensive repository of precise spatial and temporal information on chicken embryonic gene expression created through in situ hybridization. Annotations include probe sequence, stage, anatomical location of expressing tissues, citation for published images and source for unpublished curated photos. Images and annotation can improve researchersí hypotheses about gene function and genetic networks, which for a significant fraction of genes remain to be explored. As in situ hybridization information is accumulated, the GEISHA database becomes an increasingly valuable resource for the chicken biomedical and agricultural research communities.

Recent develoments :
The database has recently been redesigned to incorporate gene information from Ensembl (UK), NCBI (USA) and miRBase (USA). A comprehensive screen of the microRNA genes has been posted (Darnell et al., 2006) and we are currently conducting a comprehensive transcription factor expression screen. We are also incorporating BioMart into GEISHA to augment search and retrieval of sequence and gene annotation information.

Aknowledgement :
GEISHA is supported by grant no. R01HD044767 from the National Institutes of Health

References :
1. Darnell, D.K., Kaur S., Stanislaw S., Davey S.,. Konieczka JH, Yatskievych TA., and Antin PB. (2007) GEISHA: An In Situ Hybridization Gene Expression Resource for the Chicken Embryo. In Avian Genomics in Evolution, Agriculture and Health. Cytogenet. Genome Res. 117:30-35.
2. Antin, P.B., Kaur S., Stanislaw S., Davey S.,. Konieczka J.H., Yatskievych T.A., and Darnell D.K. (2007). Gallus Expression In Situ Hybridization Analysis (GEISHA): A chicken Embryo Gene Expression Database. Poult Sci. 86(7): 1472-1477.
3. 3. Darnell, D.K., Kaur, S, Stanislaw S., Konieczka J.H., Yatskievych T.A., and Antin P.B. (2006) MicroRNA Expression During Chick Embryo Development. Dev. Dyn. 235:3156-3165.

X:MAP

http://xmap.picr.man.ac.uk/

Description :
Annotation and visualization of genome structure for Affymetrix exon array analysis

PlasmID

http://plasmid.hms.harvard.edu/

Description :
A repository for collection and distribution of plasmid clones

EHCO

http://ehco.iis.sinica.edu.tw/

Description :
The significant advances in microarray and proteomics analyses has resulted in an exponential increase in potential new targets and has promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level. Here, we build an integrative platform, the Encyclopedia of Hepatocellular Carcinoma genes Online, dubbed EHCO, to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (~25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs. This architectural map may represent the first step toward the attempt to decipher the hepatocarcinogenesis at the systems level. Targeting hubs and/or disruption of the network formation might reveal novel strategy for HCC treatment. EHCO can be freely accessed through http://ehco.iis.sinica.edu.tw.

Aknowledgement :
This project was supported in part by grants from the National Health Research Institutes and National Science Council (Taiwan) (NSC95-2320-B-400-009-MY3) to C. F. Huang, and by the National Research Program for Genomic Medicine (NRPGM), National Science Council (Taiwan) (NSC95-3112-B-011-013-Y, Advanced Bioinformatics Core) to C. Hsu.

References :
1. Hsu CN, Lai JM, Liu CH, Tseng HH, Lin CY, Lin KT, Yeh HH, Sung TY, Hsu WL, Su LJ, Lee SA, Chen CH, Lee GC, Lee DT, Shiue YL, Yeh CW, Chang CH, Kao CY, Huang CY. (2007) Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC Bioinformatics. 2007, 8:66.

4DXpress

http://ani.embl.de/4DXpress

Description :
Database for cross species expression pattern comparisons

BloodExpress

http://hscl.cimr.cam.ac.uk/bloodexpress/

Description :
Database of Gene Expression in Mouse Haematopoiesis

CEBS

http://cebs.niehs.nih.gov/

Description :
Database of toxicogenomics, microarray and proteomics data

GPX-Macrophage

http://ebola.gti.ed.ac.uk:8090/GPX/htdocs/index.html

Description :
The GPX Macrophage Expression Atlas (GPX-MEA) is an online resource for expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. GPX Macrophage Expression Atlas (GPX-MEA) follows the MIAME standard and includes an objective quality score with each experiment. It places special emphasis on rigorously capturing the experimental design and enables the statistical analysis of expression data from different micro-array experiments. Studies may be queried on the basis of experimental parameters, sample information and quality assessment score. The ability to compare the expression values of individual genes across multiple experiments is provided. In addition, the database offers access to experimental annotation and analysis files and includes experiments and raw data previously unavailable to the public. This is the first example of a focussed macrophage gene expression database that allows efficient identification of transcriptional patterns which provide novel insights into biology of this cell system. GPX-MEA is available through the GPX website at (http://www.gti.ed.ac.uk/GPX).

Aknowledgement :
This work was supported by the Scottish Higher Education Funding Council, Biotechnology and Biological Sciences Research Council, Wellcome Trust and the European Regional Development Fund. We thank our colleagues at the GTI and collaborators Liu Bin, Ke Shuai, Reinhard Hoffmann, Xiaoyu Hu, Rachael ZoŽ Murray, Jenny Stow, Thomas Nutman, Damien Chaussabel, Daniel Popkin, Skip Virgin and Ioannis Tassiulas for contributing to this resource.

Onto-CC

http://gps-tools2.wustl.edu/onto-cc/index.html

Description :
Gene Ontology Conceptual Clustering (Onto-CC) is a tool for independent validation of gene co-expression based on GO clusters.

ProfCom

http://webclu.bio.wzw.tum.de/profcom/

Description :
Profiling of complex functionality (ProfCom) is a web based tool for the interpretation of genes that were identified to be functionally linked. Combinations of annotation terms are used to profile complex functions.

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