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Coexpression cluster:C1231: Difference between revisions

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|full_id=C1231_Melanocyte_Mallassezderived_Gingival_Keratinocyte_melanoma_Sebocyte_Mesenchymal
|full_id=C1231_Melanocyte_Mallassezderived_Gingival_Keratinocyte_melanoma_Sebocyte_Mesenchymal
|id=C1231
|id=C1231
|ontology_enrichment_celltype=CL:0000055!1.93e-16!180;CL:0000183!1.16e-11!59;CL:0000680!1.15e-10!57;CL:0000056!1.15e-10!57;CL:0000355!1.15e-10!57;CL:0000187!2.73e-10!54;CL:0000325!2.30e-09!39;CL:0000393!5.61e-09!60;CL:0000211!5.61e-09!60;CL:0000192!7.39e-07!42;CL:0000514!7.39e-07!42
|ontology_enrichment_celltype=CL:0000183!1.45e-08!59;CL:0000680!1.25e-07!58;CL:0000056!1.25e-07!58;CL:0000355!1.25e-07!58;CL:0000187!2.75e-07!55;CL:0000055!8.35e-07!106
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!9.04e-24!365;UBERON:0000119!5.47e-22!312;UBERON:0000483!2.29e-21!309;UBERON:0000481!2.97e-21!347;UBERON:0000468!1.72e-17!659;UBERON:0005256!1.36e-15!143;UBERON:0000486!2.13e-15!82;UBERON:0000914!2.11e-14!83;UBERON:0002329!2.11e-14!83;UBERON:0003077!2.11e-14!83;UBERON:0003059!2.11e-14!83;UBERON:0007282!2.11e-14!83;UBERON:0009618!2.11e-14!83;UBERON:0007285!2.11e-14!83;UBERON:0002100!4.10e-13!216;UBERON:0000922!5.14e-13!612;UBERON:0000467!5.53e-13!625;UBERON:0000477!8.14e-13!286;UBERON:0000480!1.01e-12!626;UBERON:0007023!1.24e-12!115;UBERON:0002385!2.97e-12!63;UBERON:0001015!2.97e-12!63;UBERON:0000383!2.97e-12!63;UBERON:0004290!4.05e-12!70;UBERON:0002050!4.07e-12!605;UBERON:0005423!4.07e-12!605;UBERON:0000923!5.25e-12!604;UBERON:0005291!5.25e-12!604;UBERON:0006598!5.25e-12!604;UBERON:0002532!5.25e-12!604;UBERON:0003103!6.63e-12!69;UBERON:0001134!1.41e-11!61;UBERON:0002036!1.41e-11!61;UBERON:0003082!1.41e-11!61;UBERON:0004111!1.62e-11!241;UBERON:0007100!5.01e-10!27;UBERON:0004121!1.81e-09!169;UBERON:0000064!2.99e-09!219;UBERON:0000924!3.63e-09!173;UBERON:0006601!3.63e-09!173;UBERON:0003104!5.54e-09!238;UBERON:0009142!5.54e-09!238;UBERON:0000948!7.22e-09!24;UBERON:0005498!7.22e-09!24;UBERON:0004140!7.22e-09!24;UBERON:0009881!7.22e-09!24;UBERON:0004141!7.22e-09!24;UBERON:0003084!7.22e-09!24;UBERON:0007005!7.22e-09!24;UBERON:0004139!7.22e-09!24;UBERON:0004291!7.22e-09!24;UBERON:0000033!1.20e-08!123;UBERON:0000153!2.68e-08!129;UBERON:0007811!2.68e-08!129;UBERON:0000025!3.34e-08!194;UBERON:0000062!1.05e-07!511;UBERON:0003075!1.58e-07!86;UBERON:0007284!1.58e-07!86;UBERON:0002346!4.18e-07!90;UBERON:0000479!4.74e-07!787;UBERON:0003102!5.05e-07!95
|ontology_enrichment_uberon=UBERON:0000481!2.29e-18!342;UBERON:0007023!1.79e-14!114;UBERON:0000119!3.19e-14!309;UBERON:0000483!8.49e-14!306;UBERON:0000475!9.28e-13!264;UBERON:0000477!3.55e-12!373;UBERON:0000468!9.26e-12!656;UBERON:0000486!1.57e-11!83;UBERON:0003103!1.21e-10!68;UBERON:0010314!2.88e-10!132;UBERON:0003104!5.87e-10!160;UBERON:0009142!5.87e-10!160;UBERON:0007100!6.44e-10!27;UBERON:0002385!3.66e-09!64;UBERON:0001015!3.66e-09!64;UBERON:0000383!3.66e-09!64;UBERON:0000467!1.06e-08!624;UBERON:0000948!1.40e-08!24;UBERON:0005498!1.40e-08!24;UBERON:0004140!1.40e-08!24;UBERON:0009881!1.40e-08!24;UBERON:0004141!1.40e-08!24;UBERON:0003084!1.40e-08!24;UBERON:0007005!1.40e-08!24;UBERON:0004139!1.40e-08!24;UBERON:0004291!1.40e-08!24;UBERON:0000480!1.48e-08!625;UBERON:0001134!1.50e-08!62;UBERON:0002036!1.50e-08!62;UBERON:0003082!1.50e-08!62;UBERON:0002100!1.58e-08!199;UBERON:0003077!1.88e-08!72;UBERON:0007285!1.88e-08!72;UBERON:0000922!2.06e-08!592;UBERON:0002329!2.45e-08!71;UBERON:0003059!2.45e-08!71;UBERON:0007282!2.45e-08!71;UBERON:0004290!2.45e-08!71;UBERON:0009618!2.45e-08!71;UBERON:0005423!3.55e-08!581;UBERON:0007524!4.13e-08!73;UBERON:0007503!5.32e-08!78;UBERON:0000064!6.94e-08!218;UBERON:0002050!1.09e-07!564;UBERON:0005256!1.15e-07!122;UBERON:0010371!2.35e-07!104;UBERON:0000923!8.80e-07!560;UBERON:0010316!8.80e-07!560;UBERON:0005291!8.80e-07!560;UBERON:0006598!8.80e-07!560;UBERON:0010317!8.80e-07!560;UBERON:0002532!8.80e-07!560
|tf_chipseq_enrich=USF1#7391;6:5.45271366617825:9.13505145927422e-05:0.00133155008981876
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}}
}}

Revision as of 11:01, 19 October 2012


Full id: C1231_Melanocyte_Mallassezderived_Gingival_Keratinocyte_melanoma_Sebocyte_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr17:74524635..74524670,-p@chr17:74524635..74524670
-
Hg19::chr17:74533734..74533758,-p2@CYGB
Hg19::chr17:74533763..74533773,-p5@CYGB
Hg19::chr17:74533781..74533800,-p1@CYGB
Hg19::chr17:74533963..74533981,-p3@CYGB
Hg19::chr17:74534001..74534013,-p4@CYGB
Hg19::chr17:74534029..74534039,-p6@CYGB


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
contractile cell1.45e-0859
muscle precursor cell1.25e-0758
myoblast1.25e-0758
multi-potent skeletal muscle stem cell1.25e-0758
muscle cell2.75e-0755
non-terminally differentiated cell8.35e-07106
Uber Anatomy
Ontology termp-valuen
multi-tissue structure2.29e-18342
adult organism1.79e-14114
cell layer3.19e-14309
epithelium8.49e-14306
organism subdivision9.28e-13264
anatomical cluster3.55e-12373
multi-cellular organism9.26e-12656
multilaminar epithelium1.57e-1183
compound organ1.21e-1068
structure with developmental contribution from neural crest2.88e-10132
mesenchyme5.87e-10160
entire embryonic mesenchyme5.87e-10160
primary circulatory organ6.44e-1027
muscle tissue3.66e-0964
musculature3.66e-0964
musculature of body3.66e-0964
anatomical system1.06e-08624
heart1.40e-0824
primitive heart tube1.40e-0824
primary heart field1.40e-0824
anterior lateral plate mesoderm1.40e-0824
heart tube1.40e-0824
heart primordium1.40e-0824
cardiac mesoderm1.40e-0824
cardiogenic plate1.40e-0824
heart rudiment1.40e-0824
anatomical group1.48e-08625
skeletal muscle tissue1.50e-0862
striated muscle tissue1.50e-0862
myotome1.50e-0862
trunk1.58e-08199
paraxial mesoderm1.88e-0872
presumptive paraxial mesoderm1.88e-0872
embryo2.06e-08592
somite2.45e-0871
presomitic mesoderm2.45e-0871
presumptive segmental plate2.45e-0871
dermomyotome2.45e-0871
trunk paraxial mesoderm2.45e-0871
developing anatomical structure3.55e-08581
dense mesenchyme tissue4.13e-0873
epithelial vesicle5.32e-0878
organ part6.94e-08218
embryonic structure1.09e-07564
trunk mesenchyme1.15e-07122
ecto-epithelium2.35e-07104
germ layer8.80e-07560
germ layer / neural crest8.80e-07560
embryonic tissue8.80e-07560
presumptive structure8.80e-07560
germ layer / neural crest derived structure8.80e-07560
epiblast (generic)8.80e-07560


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
USF1#739165.452713666178259.13505145927422e-050.00133155008981876



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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