TY - JOUR
T1 - eXPRESSION
T2 - An in silico tool to predict patterns of gene expression
AU - Ferguson, Deborah A.
AU - Chiang, Jing Tzyh Alan
AU - Richardson, James A.
AU - Graff, Jonathan
N1 - Funding Information:
We thank Drs Olson, Parada, Igarashi, and Garner for helpful discussions. We thank members of the Graff lab for insights, help, and reagents. This work was supported by awards to J.M.G. from the NIH, NICHD, and the March of Dimes. J.M.G. is an American Cancer Society Scholar and a Leukemia & Lymphoma Society Scholar.
PY - 2005/6
Y1 - 2005/6
N2 - In embryological studies, expression pattern analyses are of special importance since genes that have temporally and spatially restricted expression are not only essential as lineage markers but are often causative in formation of specific fates. Further, where a molecule is expressed can be quite revealing in regard to its endogenous function. We present a gene discovery tool, termed eXPRESSION, that utilizes the public EST databases to identify genes matching desired transcriptional profiles. We first tested and validated the ability of eXPRESSION to discover tissue-specific genes in the adult mouse; empirically as well as with DNA microarrays and RT-PCRs. These studies showed that eXPRESSION predictions could identify genes that are specifically expressed in adult mouse tissues. Next, we developed a novel search strategy to find genes that are expressed in specific regions or tissues of the developing mouse embryo. With these tools, we identified several novel genes that exhibited a neural-specific or neural-enriched expression pattern during murine development. The data show that eXPRESSION is widely applicable and may be used to identify both adult and embryonic tissue- or organ-specific genes with minimal cost and effort.
AB - In embryological studies, expression pattern analyses are of special importance since genes that have temporally and spatially restricted expression are not only essential as lineage markers but are often causative in formation of specific fates. Further, where a molecule is expressed can be quite revealing in regard to its endogenous function. We present a gene discovery tool, termed eXPRESSION, that utilizes the public EST databases to identify genes matching desired transcriptional profiles. We first tested and validated the ability of eXPRESSION to discover tissue-specific genes in the adult mouse; empirically as well as with DNA microarrays and RT-PCRs. These studies showed that eXPRESSION predictions could identify genes that are specifically expressed in adult mouse tissues. Next, we developed a novel search strategy to find genes that are expressed in specific regions or tissues of the developing mouse embryo. With these tools, we identified several novel genes that exhibited a neural-specific or neural-enriched expression pattern during murine development. The data show that eXPRESSION is widely applicable and may be used to identify both adult and embryonic tissue- or organ-specific genes with minimal cost and effort.
KW - Bioinformatics
KW - CNS
KW - EST profiling
KW - Gene discovery
KW - In silico
KW - Neural-specific expression
KW - Tissue-specific expression
UR - http://www.scopus.com/inward/record.url?scp=20444378522&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=20444378522&partnerID=8YFLogxK
U2 - 10.1016/j.modgep.2005.03.003
DO - 10.1016/j.modgep.2005.03.003
M3 - Article
C2 - 15939374
AN - SCOPUS:20444378522
SN - 1567-133X
VL - 5
SP - 619
EP - 628
JO - Gene Expression Patterns
JF - Gene Expression Patterns
IS - 5
ER -