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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2668_kidney_choriocarcinoma_thyroid_mesothelioma_optic_substantia_colon
|full_id=C2668_kidney_choriocarcinoma_thyroid_mesothelioma_optic_substantia_colon
|id=C2668
|id=C2668

Revision as of 15:26, 12 September 2012


Full id: C2668_kidney_choriocarcinoma_thyroid_mesothelioma_optic_substantia_colon



Phase1 CAGE Peaks

Hg19::chr2:169984040..169984044,-p@chr2:169984040..169984044
-
Hg19::chr2:170219007..170219018,-p2@LRP2
Hg19::chr2:170219037..170219050,-p1@LRP2
Hg19::chr2:170219079..170219084,-p3@LRP2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube2.59e-4857
neural rod2.59e-4857
future spinal cord2.59e-4857
neural keel2.59e-4857
neural plate8.34e-4686
presumptive neural plate8.34e-4686
neurectoderm4.36e-4490
regional part of brain1.54e-4159
adult organism2.54e-41115
central nervous system9.54e-3982
brain3.66e-3769
future brain3.66e-3769
anterior neural tube8.08e-3742
regional part of nervous system1.33e-3694
nervous system1.33e-3694
regional part of forebrain1.07e-3541
forebrain1.07e-3541
future forebrain1.07e-3541
pre-chordal neural plate2.08e-3561
telencephalon6.15e-3334
gray matter6.51e-3334
brain grey matter6.51e-3334
regional part of telencephalon8.36e-3233
cerebral hemisphere2.54e-3032
anterior region of body1.29e-24129
craniocervical region1.29e-24129
cerebral cortex7.73e-2325
pallium7.73e-2325
head8.31e-23123
regional part of cerebral cortex1.78e-2022
ectoderm-derived structure2.74e-19169
ectoderm5.50e-19173
presumptive ectoderm5.50e-19173
neocortex1.87e-1820
organ part2.45e-14219
segmental subdivision of nervous system2.14e-1213
posterior neural tube2.80e-1215
chordal neural plate2.80e-1215
tube4.25e-12194
nucleus of brain1.36e-119
neural nucleus1.36e-119
brainstem2.96e-118
basal ganglion3.65e-119
nuclear complex of neuraxis3.65e-119
aggregate regional part of brain3.65e-119
collection of basal ganglia3.65e-119
cerebral subcortex3.65e-119
segmental subdivision of hindbrain3.81e-1112
hindbrain3.81e-1112
presumptive hindbrain3.81e-1112
anatomical cluster9.30e-11286
epithelium5.90e-10309
organ1.20e-09511
cell layer1.24e-09312
multi-tissue structure1.90e-09347
telencephalic nucleus3.13e-097
organ segment1.92e-0897
larynx2.19e-089
gyrus6.29e-086
regional part of metencephalon1.11e-079
metencephalon1.11e-079
future metencephalon1.11e-079
temporal lobe2.15e-077
embryo2.50e-07612
anatomical conduit3.69e-07241
parietal lobe8.56e-075


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
HNF4A#3172317.34921777221530.0003125641557482750.0032155129887898
HNF4G#3174321.56506689483510.0001638032421292610.00203684329143206
SUZ12#23512337.58683568329723.12785741999833e-050.000631857448911422



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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