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Coexpression cluster:C2356: Difference between revisions

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|tf_chipseq_enrich=ESR1#2099;2:15.3843016480772:0.00606557262969351:0.026835649405768!SREBF1#6720;2:23.5029247202441:0.00263845490076824:0.0145828530578606
|tf_chipseq_enrich=ESR1#2099;2:15.3843016480772:0.00606557262969351:0.026835649405768!SREBF1#6720;2:23.5029247202441:0.00263845490076824:0.0145828530578606
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}}
}}

Revision as of 15:26, 26 November 2012


Full id: C2356_cerebellum_pineal_small_pons_medial_globus_brain



Phase1 CAGE Peaks

Hg19::chr15:91643424..91643440,+p11@SV2B
Hg19::chr6:166253676..166253680,-p@chr6:166253676..166253680
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Hg19::chr7:26415791..26415799,-p2@ENST00000451368
Hg19::chr7:26415806..26415813,-p3@ENST00000451368


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


GO IDGO nameFDR corrected p-value
GO:0001669acrosome0.0219003885552808
GO:0008021synaptic vesicle0.0237254209348875
GO:0006836neurotransmitter transport0.0237254209348875
GO:0030136clathrin-coated vesicle0.0262348404568468
GO:0030135coated vesicle0.0263326100486115
GO:0005764lysosome0.0263326100486115
GO:0000323lytic vacuole0.0263326100486115
GO:0005773vacuole0.0265770340280231
GO:0016023cytoplasmic membrane-bound vesicle0.0303236149226965
GO:0031988membrane-bound vesicle0.0303236149226965
GO:0031410cytoplasmic vesicle0.0303236149226965
GO:0030054cell junction0.0303236149226965
GO:0031982vesicle0.0303236149226965



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 tube2.13e-8356
neural rod2.13e-8356
future spinal cord2.13e-8356
neural keel2.13e-8356
regional part of nervous system5.05e-7753
regional part of brain5.05e-7753
central nervous system2.15e-6681
regional part of forebrain3.20e-6541
forebrain3.20e-6541
anterior neural tube3.20e-6541
future forebrain3.20e-6541
brain6.04e-6568
future brain6.04e-6568
nervous system1.74e-5889
neural plate2.68e-5882
presumptive neural plate2.68e-5882
neurectoderm5.54e-5586
brain grey matter1.81e-4934
gray matter1.81e-4934
telencephalon9.80e-4934
ecto-epithelium2.41e-47104
pre-chordal neural plate5.04e-4661
regional part of telencephalon7.56e-4532
cerebral hemisphere8.47e-4532
adult organism1.45e-44114
regional part of cerebral cortex4.97e-3922
structure with developmental contribution from neural crest3.66e-36132
neocortex9.86e-3520
cerebral cortex7.66e-3425
pallium7.66e-3425
ectoderm-derived structure1.87e-29171
ectoderm1.87e-29171
presumptive ectoderm1.87e-29171
organ system subdivision9.56e-25223
tube1.06e-22192
posterior neural tube1.64e-1815
chordal neural plate1.64e-1815
diencephalon2.31e-187
future diencephalon2.31e-187
anatomical conduit3.07e-18240
neural nucleus4.52e-179
nucleus of brain4.52e-179
gyrus1.38e-146
anatomical cluster3.39e-14373
basal ganglion5.15e-139
nuclear complex of neuraxis5.15e-139
aggregate regional part of brain5.15e-139
collection of basal ganglia5.15e-139
cerebral subcortex5.15e-139
segmental subdivision of hindbrain6.73e-1312
hindbrain6.73e-1312
presumptive hindbrain6.73e-1312
parietal lobe1.45e-125
telencephalic nucleus1.96e-127
epithelium6.93e-12306
segmental subdivision of nervous system8.80e-1213
cell layer1.23e-11309
regional part of diencephalon2.33e-114
gland of diencephalon2.39e-114
neuroendocrine gland2.39e-114
multi-tissue structure3.88e-11342
organ part1.89e-10218
regional part of metencephalon2.01e-109
metencephalon2.01e-109
future metencephalon2.01e-109
brainstem2.13e-106
temporal lobe6.90e-096
occipital lobe1.13e-085
organ1.81e-08503
pons1.87e-083
male genital duct2.23e-083
internal male genitalia2.23e-083
limbic system2.83e-085
frontal cortex3.15e-083
spinal cord9.15e-083
dorsal region element9.15e-083
dorsum9.15e-083
pineal body9.52e-072
regional part of epithalamus9.52e-072
secretory circumventricular organ9.52e-072
circumventricular organ9.52e-072
epithalamus9.52e-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


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

TF#promotersEnrichmentp-valueq-value
ESR1#2099215.38430164807720.006065572629693510.026835649405768
SREBF1#6720223.50292472024410.002638454900768240.0145828530578606



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.