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Coexpression cluster:C2132

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Full id: C2132_cerebellum_putamen_pituitary_merkel_gastrointestinal_brain_iPS



Phase1 CAGE Peaks

Hg19::chr11:45907236..45907257,+p3@MAPK8IP1
Hg19::chr8:104511921..104511933,+p@chr8:104511921..104511933
+
Hg19::chr8:104511965..104511977,+p@chr8:104511965..104511977
+
Hg19::chr8:104512000..104512015,+p@chr8:104512000..104512015
+


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>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
embryonic stem cell3.98e-075
Uber Anatomy
Ontology termp-valuen
neural tube2.95e-4756
neural rod2.95e-4756
future spinal cord2.95e-4756
neural keel2.95e-4756
nervous system4.77e-4789
regional part of nervous system1.12e-4653
regional part of brain1.12e-4653
central nervous system8.37e-4681
regional part of forebrain1.70e-4041
forebrain1.70e-4041
anterior neural tube1.70e-4041
future forebrain1.70e-4041
brain2.03e-4068
future brain2.03e-4068
brain grey matter9.40e-3334
gray matter9.40e-3334
telencephalon1.07e-3234
cerebral hemisphere2.99e-3132
neural plate8.57e-3182
presumptive neural plate8.57e-3182
regional part of telencephalon8.71e-3132
neurectoderm1.68e-2886
regional part of cerebral cortex3.23e-2722
pre-chordal neural plate4.05e-2761
neocortex3.08e-2520
ecto-epithelium3.85e-25104
organ system subdivision8.74e-25223
adult organism8.96e-24114
cerebral cortex4.59e-2325
pallium4.59e-2325
ectoderm-derived structure9.36e-23171
ectoderm9.36e-23171
presumptive ectoderm9.36e-23171
structure with developmental contribution from neural crest9.56e-17132
basal ganglion2.35e-119
nuclear complex of neuraxis2.35e-119
aggregate regional part of brain2.35e-119
collection of basal ganglia2.35e-119
cerebral subcortex2.35e-119
neural nucleus3.71e-119
nucleus of brain3.71e-119
anatomical cluster9.69e-10373
tube1.69e-09192
telencephalic nucleus2.87e-097
diencephalon3.73e-097
future diencephalon3.73e-097
temporal lobe4.12e-096
organ part1.12e-08218
posterior neural tube1.81e-0815
chordal neural plate1.81e-0815
gyrus2.72e-086
anatomical conduit9.44e-08240
segmental subdivision of hindbrain1.03e-0712
hindbrain1.03e-0712
presumptive hindbrain1.03e-0712
parietal lobe1.53e-075
occipital lobe2.89e-075
brainstem3.15e-076
segmental subdivision of nervous system6.07e-0713
limbic system6.11e-075
Disease
Ontology termp-valuen
respiratory system cancer2.09e-0716


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
CTCF#1066445.360256373075030.001211145381643620.00815753982416344
JUND#372735.245997956403270.01043432751748420.0386655808827183



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.