CRONOS: the cross-reference navigation server

Summary: Cross-mapping of gene and protein identifiers between different databases is a tedious and time-consuming task. To overcome this, we developed CRONOS, a cross-reference server that contains entries from five mammalian organisms presented by major gene and protein information resources. Sequence similarity analysis of the mapped entries shows that the cross-references are highly accurate. In total, up to 18 different identifier types can be used for identification of cross-references. The quality of the mapping could be improved substantially by exclusion of ambiguous gene and protein names which were manually validated. Organism-specific lists of ambiguous terms, which are valuable for a variety of bioinformatics applications like text mining are available for download

OREST: the online resource for EST analysis

The generation of expressed sequence tag (EST) libraries offers an affordable approach to investigate organisms, if no genome sequence is available. OREST (http://mips.gsf.de/genre/proj/orest/index.html) is a server-based EST analysis pipeline, which allows the rapid analysis of large amounts of ESTs or cDNAs from mammalia and fungi. In order to assign the ESTs to genes or proteins OREST maps DNA sequences to reference datasets of gene products and in a second step to complete genome sequences. Mapping against genome sequences recovers additional 13% of EST data, which otherwise would escape further analysis. To enable functional analysis of the datasets, ESTs are functionally annotated using the hierarchical FunCat annotation scheme as well as GO annotation terms. OREST also allows to predict the association of gene products and diseases by Morbid Map (OMIM) classification. A statistical analysis of the results of the dataset is possible with the included PROMPT software, which provides information about enrichment and depletion of functional and disease annotation terms. OREST was successfully applied for the identification and functional characterization of more than 3000 EST sequences of the common marmoset monkey (Callithrix jacchus) as part of an international collaboration

CORUM: the comprehensive resource of mammalian protein complexes—2009

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The new CORUM 2.0 release encompasses 2837 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes. The CORUM dataset is built from 3198 different genes, representing ∼16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. Recent developments include mapping of functional annotation to Gene Ontology terms as well as cross-references to Entrez Gene identifiers. In addition, a ‘Phylogenetic Conservation’ analysis tool was implemented that analyses the potential occurrence of orthologous protein complex subunits in mammals and other selected groups of organisms. This allows one to predict the occurrence of protein complexes in different phylogenetic groups. CORUM is freely accessible at (http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html)

Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate

Contains fulltext : 34911.pdf (publisher's version ) (Open Access)BACKGROUND: The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug development and safety assessment. In contrast to the growing interest for the marmoset as an animal model, the molecular tools for genetic analysis are extremely limited. RESULTS: Here we report the development of the first marmoset-specific oligonucleotide microarray (EUMAMA) containing probe sets targeting 1541 different marmoset transcripts expressed in hippocampus. These 1541 transcripts represent a wide variety of different functional gene classes. Hybridisation of the marmoset microarray with labelled RNA from hippocampus, cortex and a panel of 7 different peripheral tissues resulted in high detection rates of 85% in the neuronal tissues and on average 70% in the non-neuronal tissues. The expression profiles of the 2 neuronal tissues, hippocampus and cortex, were highly similar, as indicated by a correlation coefficient of 0.96. Several transcripts with a tissue-specific pattern of expression were identified. Besides the marmoset microarray we have generated 3215 ESTs derived from marmoset hippocampus, which have been annotated and submitted to GenBank [GenBank: EF214838-EF215447, EH380242-EH382846]. CONCLUSION: We have generated the first marmoset-specific DNA microarray and demonstrated its use to characterise large-scale gene expression profiles of hippocampus but also of other neuronal and non-neuronal tissues. In addition, we have generated a large collection of ESTs of marmoset origin, which are now available in the public domain. These new tools will facilitate molecular genetic research into this non-human primate animal model

doi:10.1093/nar/gkn253 OREST: the online resource for EST analysis

The generation of expressed sequence tag (EST) libraries offers an affordable approach to investigate organisms, if no genome sequence is available. ORES

SOFTWARE Open Access CIDeR: multifactorial interaction networks in human diseases

The pathobiology of common diseases is influenced by heterogeneous factors interacting in complex networks. CIDe

CORUM: the comprehensive resource of

mammalian protein complexe

Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate-1

<p><b>Copyright information:</b></p><p>Taken from "Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate"</p><p>http://www.biomedcentral.com/1471-2164/8/190</p><p>BMC Genomics 2007;8():190-190.</p><p>Published online 25 Jun 2007</p><p>PMCID:PMC1929077.</p><p></p>y the correlation coefficient

Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate-2

<p><b>Copyright information:</b></p><p>Taken from "Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate"</p><p>http://www.biomedcentral.com/1471-2164/8/190</p><p>BMC Genomics 2007;8():190-190.</p><p>Published online 25 Jun 2007</p><p>PMCID:PMC1929077.</p><p></p>total of 1932 (60%) ESTs were assigned a gene name, 610 (19%) contained a partial ORF, 642 (20%) were mappable to a genome but could not be assigned a gene name and 31 (1%) could not be mapped. . Pie chart indicating the origin of the marmoset sequences represented on the marmoset microarray. Of the in total 1541 marmoset transcripts represented on the array the majority (1445 = 95%) were derived from the set of 3215 marmoset ESTs submitted to GenBank. The remaining 5% consisted of 68 pre-existing marmoset sequences already present in GenBank and 28 ESTs from the hippocampal cDNA library that were not submitted to GenBank. The 1445 submitted ESTs could be subdivided into a group of 886 (58%) that were assigned a gene name, 364 (24%) with a (partial) ORF, 188 (12%) that were mappable but without a gene name or an ORF and 7 (0%) that were not mappable

Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate-0

<p><b>Copyright information:</b></p><p>Taken from "Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate"</p><p>http://www.biomedcentral.com/1471-2164/8/190</p><p>BMC Genomics 2007;8():190-190.</p><p>Published online 25 Jun 2007</p><p>PMCID:PMC1929077.</p><p></p>total of 1932 (60%) ESTs were assigned a gene name, 610 (19%) contained a partial ORF, 642 (20%) were mappable to a genome but could not be assigned a gene name and 31 (1%) could not be mapped. . Pie chart indicating the origin of the marmoset sequences represented on the marmoset microarray. Of the in total 1541 marmoset transcripts represented on the array the majority (1445 = 95%) were derived from the set of 3215 marmoset ESTs submitted to GenBank. The remaining 5% consisted of 68 pre-existing marmoset sequences already present in GenBank and 28 ESTs from the hippocampal cDNA library that were not submitted to GenBank. The 1445 submitted ESTs could be subdivided into a group of 886 (58%) that were assigned a gene name, 364 (24%) with a (partial) ORF, 188 (12%) that were mappable but without a gene name or an ORF and 7 (0%) that were not mappable