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Coexpression cluster:C3140

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Full id: C3140_argyrophil_Lens_Ciliary_eye_small_Astrocyte_Iris



Phase1 CAGE Peaks

Hg19::chr11:31827535..31827565,-p11@PAX6
Hg19::chr11:31839453..31839462,-p9@PAX6
Hg19::chr11:31839488..31839515,-p3@PAX6


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><br>


Uber Anatomy
Ontology termp-valuen
neural plate2.10e-10482
presumptive neural plate2.10e-10482
neurectoderm8.90e-9986
neural tube3.30e-9756
neural rod3.30e-9756
future spinal cord3.30e-9756
neural keel3.30e-9756
central nervous system9.33e-9381
regional part of nervous system1.90e-9053
regional part of brain1.90e-9053
pre-chordal neural plate1.10e-8761
nervous system5.58e-8289
ecto-epithelium9.17e-79104
brain3.87e-7668
future brain3.87e-7668
regional part of forebrain9.54e-7241
forebrain9.54e-7241
anterior neural tube9.54e-7241
future forebrain9.54e-7241
structure with developmental contribution from neural crest1.17e-62132
telencephalon4.04e-6234
brain grey matter7.75e-6234
gray matter7.75e-6234
ectoderm-derived structure1.98e-58171
ectoderm1.98e-58171
presumptive ectoderm1.98e-58171
regional part of telencephalon2.77e-5832
cerebral hemisphere4.03e-5832
cerebral cortex2.26e-4825
pallium2.26e-4825
neocortex1.66e-4120
regional part of cerebral cortex1.76e-4122
adult organism4.33e-35114
organ system subdivision5.20e-30223
posterior neural tube3.96e-2515
chordal neural plate3.96e-2515
anatomical cluster1.65e-23373
organ part1.38e-21218
tube2.48e-20192
pigment epithelium of eye3.00e-2011
eye1.36e-1921
visual system1.36e-1921
segmental subdivision of hindbrain6.18e-1912
hindbrain6.18e-1912
presumptive hindbrain6.18e-1912
epithelium7.64e-19306
cell layer1.72e-18309
camera-type eye1.30e-1720
simple eye1.30e-1720
immature eye1.30e-1720
ocular region1.30e-1720
eyeball of camera-type eye1.30e-1720
optic cup1.30e-1720
optic vesicle1.30e-1720
eye primordium1.30e-1720
segmental subdivision of nervous system2.76e-1713
sense organ1.17e-1624
sensory system1.17e-1624
entire sense organ system1.17e-1624
anterior segment of eyeball3.96e-1614
face1.08e-1522
basal ganglion4.97e-159
nuclear complex of neuraxis4.97e-159
aggregate regional part of brain4.97e-159
collection of basal ganglia4.97e-159
cerebral subcortex4.97e-159
temporal lobe6.40e-156
multi-tissue structure1.00e-14342
neural nucleus1.13e-149
nucleus of brain1.13e-149
regional part of metencephalon8.28e-149
metencephalon8.28e-149
future metencephalon8.28e-149
anatomical conduit1.86e-13240
gyrus1.13e-126
occipital lobe5.55e-125
brainstem9.28e-126
telencephalic nucleus2.64e-117
atypical epithelium6.16e-114
diencephalon7.97e-117
future diencephalon7.97e-117
parietal lobe1.41e-105
embryo2.00e-10592
germ layer2.98e-10560
germ layer / neural crest2.98e-10560
embryonic tissue2.98e-10560
presumptive structure2.98e-10560


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
SUZ12#23512350.11578091106297.93834897779404e-060.000221381369530529



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.