Human Gene Set: GCNP_SHH_UP_EARLY.V1_DN


Standard name GCNP_SHH_UP_EARLY.V1_DN
Systematic name M2638
Brief description Genes down-regulated in granule cell neuron precursors (GCNPs) after stimulation with Shh for 3h.
Full description or abstract Hedgehog pathway activation is required for proliferation of cerebellar granule cell neuron precursors during development and is etiologic in certain cerebellar tumors. To identify genes expressed specifically in granule cell neuron precursors, we used oligonucleotide microarrays to analyze regulation of 13,179 genes/expressed sequence tags in heterogeneous primary cultures of neonatal mouse cerebellum that respond to the mitogen Sonic hedgehog. In conjunction, we applied experiment-specific noise models to render a gene-by-gene robust indication of up-regulation in Sonic hedgehog-treated cultures. Twelve genes so identified were tested, and 10 (83%) showed appropriate expression in the external granular layer (EGL) of the postnatal day (PN) 7 cerebellum and down-regulation by PN 15, as verified by in situ hybridization. Whole-organ profiling of the developing cerebellum was carried out from PN 1 to 30 to generate a database of temporal gene regulation profiles (TRPs). From the database an algorithm was developed to capture the TRP typical of EGL-specific genes. The "TRP-EGL" accurately predicted expression in vivo of an additional 18 genes/expressed sequence tags with a sensitivity of 80% and a specificity of 88%. We then compared the positive predictive value of our analytical procedure with other widely used methods, as verified by the TRP-EGL in silico. These findings suggest that replicate experiments and incorporation of noise models increase analytical specificity. They further show that genome-wide methods are an effective means to identify stage-specific gene expression in the developing granule cell lineage.
Collection C6: Oncogenic Signature
Source publication Pubmed 11960025   Authors: Zhao Q,Kho A,Kenney AM,Yuk Di DI,Kohane I,Rowitch DH
Exact source early (3 h) GCNP SHH+ vs VEHICLE; bottom 200 genes (diff. of means)
Related gene sets (show 3 additional gene sets from the source publication)

(show 2 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Mus musculus
Contributed by Pablo Tamayo (Broad Institute)
Source platform or
identifier namespace		 HUMAN_GENE_SYMBOL
Dataset references (show 1 datasets)
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 167 genes
Gene families ? Categorize these 167 genes by gene family
Show members (show 200 source identifiers mapped to 167 genes)
Version history 7.1: Fixed RIKEN identifiers.

See MSigDB license terms here. Please note that certain gene sets have special access terms.