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Coexpression cluster:C1058: Difference between revisions

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|tf_chipseq_enrich=SUZ12#23512;5:31.3223630694143:1.68017316924325e-07:9.26481550277698e-06
|tf_chipseq_enrich=SUZ12#23512;5:31.3223630694143:1.68017316924325e-07:9.26481550277698e-06
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}}
}}

Revision as of 14:39, 26 November 2012


Full id: C1058_cerebellum_parietal_occipital_pineal_brain_retinoblastoma_temporal



Phase1 CAGE Peaks

Hg19::chr19:10515584..10515599,+p@chr19:10515584..10515599
+
Hg19::chr1:57889966..57889983,-p6@DAB1
Hg19::chr8:9760906..9760907,-p1@ENST00000517675
Hg19::chr8:9763201..9763208,-p7@ENST00000521242
Hg19::chr8:9763221..9763232,-p4@ENST00000521242
Hg19::chr8:9763242..9763268,-p1@ENST00000521242
Hg19::chr8:9763271..9763300,-p3@ENST00000521242
Hg19::chr8:9763301..9763343,-p2@ENST00000521242


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>

Cell Type
Ontology termp-valuen
neuronal stem cell8.08e-128
neuron1.14e-116
neuroblast1.14e-116
electrically signaling cell1.14e-116
embryonic stem cell7.96e-095
Uber Anatomy
Ontology termp-valuen
central nervous system9.89e-8181
nervous system1.20e-7889
neural tube1.20e-7156
neural rod1.20e-7156
future spinal cord1.20e-7156
neural keel1.20e-7156
regional part of nervous system1.67e-6653
regional part of brain1.67e-6653
brain1.74e-6168
future brain1.74e-6168
regional part of forebrain1.99e-5441
forebrain1.99e-5441
anterior neural tube1.99e-5441
future forebrain1.99e-5441
neural plate2.73e-5182
presumptive neural plate2.73e-5182
neurectoderm3.32e-5086
cerebral hemisphere1.40e-4832
brain grey matter1.91e-4834
gray matter1.91e-4834
telencephalon2.16e-4834
regional part of telencephalon5.74e-4532
regional part of cerebral cortex1.08e-4122
pre-chordal neural plate6.44e-4061
neocortex7.33e-3820
ecto-epithelium2.74e-37104
ectoderm-derived structure1.18e-36171
ectoderm1.18e-36171
presumptive ectoderm1.18e-36171
cerebral cortex4.87e-3625
pallium4.87e-3625
adult organism8.14e-31114
structure with developmental contribution from neural crest3.32e-30132
organ system subdivision4.53e-27223
posterior neural tube1.46e-1715
chordal neural plate1.46e-1715
tube2.46e-14192
basal ganglion7.27e-149
nuclear complex of neuraxis7.27e-149
aggregate regional part of brain7.27e-149
collection of basal ganglia7.27e-149
cerebral subcortex7.27e-149
neural nucleus1.27e-139
nucleus of brain1.27e-139
gyrus3.14e-136
segmental subdivision of hindbrain6.58e-1312
hindbrain6.58e-1312
presumptive hindbrain6.58e-1312
anatomical cluster2.64e-12373
segmental subdivision of nervous system9.32e-1213
brainstem1.23e-116
parietal lobe1.79e-115
occipital lobe4.30e-115
temporal lobe5.33e-116
limbic system5.40e-115
telencephalic nucleus2.80e-107
regional part of diencephalon2.88e-094
corpus striatum5.57e-094
striatum5.57e-094
ventral part of telencephalon5.57e-094
future corpus striatum5.57e-094
anatomical conduit7.29e-09240
regional part of metencephalon1.94e-089
metencephalon1.94e-089
future metencephalon1.94e-089
organ part8.80e-08218
diencephalon1.49e-077
future diencephalon1.49e-077
frontal cortex1.76e-073
caudate-putamen4.31e-073
dorsal striatum4.31e-073
pons7.93e-073


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#23512531.32236306941431.68017316924325e-079.26481550277698e-06



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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