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As mentioned above, such links include external resources such as NCBI Entrez, Ensembl, iHOP, Pubgene, MEM - Multi Experiment Matrix, and a number of genomics and stem cell databases.
To facilitate data comparison between the FunGenES database and other resources, we have included a series of links to other Stem cell databases, i.e., to SCDb, Amazonia in the Study your Gene(s) of Interest search engine.
Thus, although we have used a different microarray platform, the genes defined as stem cell-specific in our system (e.g. the 144 Unigene clusters that belonged to group of genes down-regulated after dox withdrawal), reveal a 21 and 23%% overlap with genes defined as HSC-specific in the two different stem cell databases, respectively (see Additional file 4).
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Type A genes were further matched to the Stem Cell Database (http://stemcell.princeton.edu [17] to reveal any specificity to the characteristic properties of FL hematopoiesis.
In this study, we have integrated our datasets with existing related datasets from both human and mouse ES and EC cells to generate an Embryonic Stem Cell Database (ESCDb).
In the current era of systems biology driven research, we envisage that our integrated embryonic stem cell database will prove beneficial to the booming field of ES, iPS and cancer research.
To facilitate this, we have integrated our datasets along with existing related datasets from both human and mouse ES and EC cells to generate an Embryonic Stem Cell Database (ESCDb) which allows rapid and convenient access and comparisons between published datasets related to embryonic stem cell biology.
We compared our 484 target genes identified by microarray analysis to the published stem cell database where Ivanova et al. [25] mapped mRNA expression profiles of hematopoietic stem cells of various phenotypically defined hierarchical levels or clusters including LT-HSC, ST-HSC, and early-intermediate-late progenitors.
In order to facilitate the construction of this database, we gathered previously published datasets together with ChIP-on-chip using OCT4 and the NCCIT cell line described in this present work to establish the Embryonic Stem Cell Database (http://biit.cs.ut.ee/escd/).ee/escd/
The data are deposited in the Stem Cell Database under accession number StemDB-2316 (http://www.stemdb.org/stemdb/utils/show?id=StemDB-2316 id=StemDB-2316
The Embryonic Stem Cell Database (ESCD) has mainly collected datasets on key transcription factor binding, RNAi knockdown, and protein overexpression experiments [18].
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