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Coexpression cluster:C1767: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249716124846152!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298757343238142!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386610553480954
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249716124846152!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298757343238142!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386610553480954
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}}
}}

Revision as of 15:05, 26 November 2012


Full id: C1767_occipital_temporal_cerebellum_postcentral_insula_amygdala_paracentral



Phase1 CAGE Peaks

Hg19::chr16:85061367..85061430,+p1@KIAA0513
Hg19::chr7:127671476..127671495,-p7@LRRC4
Hg19::chr7:127672114..127672133,-p4@LRRC4
Hg19::chr7:127672146..127672170,-p3@LRRC4
Hg19::chr7:127672173..127672191,-p1@LRRC4


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
adult organism2.91e-41114
neural tube2.86e-3756
neural rod2.86e-3756
future spinal cord2.86e-3756
neural keel2.86e-3756
central nervous system1.58e-3681
regional part of nervous system2.07e-3553
regional part of brain2.07e-3553
nervous system8.20e-3589
regional part of forebrain1.51e-3241
forebrain1.51e-3241
anterior neural tube1.51e-3241
future forebrain1.51e-3241
brain6.66e-3168
future brain6.66e-3168
telencephalon1.38e-2734
brain grey matter3.79e-2734
gray matter3.79e-2734
neural plate5.03e-2782
presumptive neural plate5.03e-2782
cerebral hemisphere2.08e-2632
neurectoderm2.61e-2686
regional part of telencephalon5.41e-2632
pre-chordal neural plate3.81e-2361
regional part of cerebral cortex1.20e-2122
cerebral cortex1.46e-2025
pallium1.46e-2025
neocortex5.16e-2020
ecto-epithelium7.96e-18104
ectoderm-derived structure1.06e-16171
ectoderm1.06e-16171
presumptive ectoderm1.06e-16171
organ system subdivision3.44e-14223
germ layer6.29e-14560
germ layer / neural crest6.29e-14560
embryonic tissue6.29e-14560
presumptive structure6.29e-14560
germ layer / neural crest derived structure6.29e-14560
epiblast (generic)6.29e-14560
structure with developmental contribution from neural crest7.79e-14132
bone marrow9.24e-1476
developing anatomical structure1.14e-13581
embryo1.35e-13592
embryonic structure2.15e-13564
immune system2.23e-1393
hematopoietic system5.37e-1398
blood island5.37e-1398
hemolymphoid system1.63e-12108
anatomical system9.97e-12624
anatomical group1.32e-11625
bone element1.39e-1182
multi-cellular organism2.39e-11656
organ5.31e-11503
skeletal element3.20e-0990
basal ganglion1.15e-089
nuclear complex of neuraxis1.15e-089
aggregate regional part of brain1.15e-089
collection of basal ganglia1.15e-089
cerebral subcortex1.15e-089
skeletal system1.50e-08100
neural nucleus5.29e-089
nucleus of brain5.29e-089
tissue1.49e-07773
temporal lobe2.69e-076
gyrus3.65e-076
tube3.98e-07192
telencephalic nucleus6.74e-077


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#1066455.360256373075030.0002259278299937090.00249716124846152
E2F1#186943.925911371903460.007214984547106360.0298757343238142
RAD21#588548.284027116365060.0004011622639122450.00386610553480954



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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