Personal tools

Coexpression cluster:C1732

From FANTOM5_SSTAR

Revision as of 11:38, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1732_parietal_maxillary_temporal_occipital_small_medial_putamen



Phase1 CAGE Peaks

Hg19::chr14:79489466..79489481,+p@chr14:79489466..79489481
+
Hg19::chr14:79497000..79497004,+p@chr14:79497000..79497004
+
Hg19::chr14:79511184..79511189,+p@chr14:79511184..79511189
+
Hg19::chr14:79667198..79667202,+p@chr14:79667198..79667202
+
Hg19::chr14:79731597..79731601,+p@chr14:79731597..79731601
+


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 tube8.35e-8556
neural rod8.35e-8556
future spinal cord8.35e-8556
neural keel8.35e-8556
regional part of nervous system3.20e-7853
regional part of brain3.20e-7853
central nervous system2.17e-7181
regional part of forebrain2.29e-7141
forebrain2.29e-7141
anterior neural tube2.29e-7141
future forebrain2.29e-7141
brain grey matter1.91e-6834
gray matter1.91e-6834
telencephalon3.45e-6834
cerebral hemisphere7.47e-6432
brain9.92e-6468
future brain9.92e-6468
regional part of telencephalon1.28e-6332
nervous system4.90e-6389
neural plate2.36e-5982
presumptive neural plate2.36e-5982
neurectoderm1.53e-5886
regional part of cerebral cortex1.02e-5322
pre-chordal neural plate2.57e-5061
neocortex1.09e-4820
ecto-epithelium1.12e-48104
cerebral cortex9.67e-4725
pallium9.67e-4725
adult organism3.14e-37114
structure with developmental contribution from neural crest3.15e-37132
ectoderm-derived structure7.86e-34171
ectoderm7.86e-34171
presumptive ectoderm7.86e-34171
organ system subdivision4.89e-25223
basal ganglion2.07e-239
nuclear complex of neuraxis2.07e-239
aggregate regional part of brain2.07e-239
collection of basal ganglia2.07e-239
cerebral subcortex2.07e-239
neural nucleus5.46e-239
nucleus of brain5.46e-239
tube1.75e-20192
telencephalic nucleus2.58e-187
gyrus2.40e-166
posterior neural tube7.66e-1515
chordal neural plate7.66e-1515
parietal lobe3.65e-145
limbic system4.53e-145
occipital lobe5.31e-145
temporal lobe6.25e-146
anatomical conduit6.89e-14240
epithelium1.20e-13306
cell layer2.22e-13309
organ part6.01e-12218
corpus striatum1.31e-114
striatum1.31e-114
ventral part of telencephalon1.31e-114
future corpus striatum1.31e-114
anatomical cluster3.37e-11373
brainstem1.45e-106
segmental subdivision of hindbrain1.74e-0912
hindbrain1.74e-0912
presumptive hindbrain1.74e-0912
multi-tissue structure1.76e-09342
frontal cortex2.65e-093
caudate-putamen2.88e-093
dorsal striatum2.88e-093
segmental subdivision of nervous system1.13e-0813
pons1.21e-083
spinal cord5.45e-083
dorsal region element5.45e-083
dorsum5.45e-083
regional part of metencephalon5.17e-079
metencephalon5.17e-079
future metencephalon5.17e-079
amygdala8.80e-072
middle frontal gyrus9.05e-072


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


No analysis results for this cluster

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.