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Coexpression cluster:C528: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001949!1.38e-16!3;UBERON:0004815!2.43e-15!3;UBERON:0002031!2.43e-15!3;UBERON:0003102!5.61e-14!99;UBERON:0001708!1.12e-12!4;UBERON:0008895!1.12e-12!4;UBERON:0001911!6.13e-12!4;UBERON:0005333!6.13e-12!4;UBERON:0008425!6.13e-12!4;UBERON:0005311!6.13e-12!4;UBERON:0001004!1.22e-11!74;UBERON:0002419!1.72e-11!2;UBERON:0007771!1.72e-11!2;UBERON:0003297!1.72e-11!2;UBERON:0001821!1.72e-11!2;UBERON:0003487!1.72e-11!2;UBERON:0001820!1.72e-11!2;UBERON:0005089!1.72e-11!2;UBERON:0005088!1.72e-11!2;UBERON:0000033!2.06e-10!56;UBERON:0011159!3.15e-10!5;UBERON:0004119!9.75e-10!160;UBERON:0000925!9.75e-10!160;UBERON:0006595!9.75e-10!160;UBERON:0003729!1.31e-09!13;UBERON:0000365!1.88e-09!5;UBERON:0002185!2.11e-09!5;UBERON:0000153!3.58e-09!62;UBERON:0007811!3.58e-09!62;UBERON:0010188!1.37e-08!6;UBERON:0002539!1.37e-08!6;UBERON:0008816!1.37e-08!6;UBERON:0005157!1.57e-08!47;UBERON:0001003!1.80e-08!15;UBERON:0007376!1.80e-08!15;UBERON:0007383!1.80e-08!15;UBERON:0007196!5.11e-08!15;UBERON:0001558!5.11e-08!15;UBERON:0005910!5.99e-08!6;UBERON:0000166!1.34e-07!22;UBERON:0000161!1.49e-07!36;UBERON:0000165!1.65e-07!29;UBERON:0000930!1.65e-07!29;UBERON:0005153!2.70e-07!37;UBERON:0005085!5.43e-07!31;UBERON:0002365!5.54e-07!31;UBERON:0002330!5.54e-07!31
|ontology_enrichment_uberon=UBERON:0001949!1.38e-16!3;UBERON:0004815!2.43e-15!3;UBERON:0002031!2.43e-15!3;UBERON:0003102!5.61e-14!99;UBERON:0001708!1.12e-12!4;UBERON:0008895!1.12e-12!4;UBERON:0001911!6.13e-12!4;UBERON:0005333!6.13e-12!4;UBERON:0008425!6.13e-12!4;UBERON:0005311!6.13e-12!4;UBERON:0001004!1.22e-11!74;UBERON:0002419!1.72e-11!2;UBERON:0007771!1.72e-11!2;UBERON:0003297!1.72e-11!2;UBERON:0001821!1.72e-11!2;UBERON:0003487!1.72e-11!2;UBERON:0001820!1.72e-11!2;UBERON:0005089!1.72e-11!2;UBERON:0005088!1.72e-11!2;UBERON:0000033!2.06e-10!56;UBERON:0011159!3.15e-10!5;UBERON:0004119!9.75e-10!160;UBERON:0000925!9.75e-10!160;UBERON:0006595!9.75e-10!160;UBERON:0003729!1.31e-09!13;UBERON:0000365!1.88e-09!5;UBERON:0002185!2.11e-09!5;UBERON:0000153!3.58e-09!62;UBERON:0007811!3.58e-09!62;UBERON:0010188!1.37e-08!6;UBERON:0002539!1.37e-08!6;UBERON:0008816!1.37e-08!6;UBERON:0005157!1.57e-08!47;UBERON:0001003!1.80e-08!15;UBERON:0007376!1.80e-08!15;UBERON:0007383!1.80e-08!15;UBERON:0007196!5.11e-08!15;UBERON:0001558!5.11e-08!15;UBERON:0005910!5.99e-08!6;UBERON:0000166!1.34e-07!22;UBERON:0000161!1.49e-07!36;UBERON:0000165!1.65e-07!29;UBERON:0000930!1.65e-07!29;UBERON:0005153!2.70e-07!37;UBERON:0005085!5.43e-07!31;UBERON:0002365!5.54e-07!31;UBERON:0002330!5.54e-07!31
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|tfbs_overrepresentation_for_novel_motifs=0.144412,0.000333902,0.139625,0.241986,0.364884,0.675949,0.300393,0.0518257,0.189397,0.118722,0.218065,1.60153,0.137255,0.291158,0.362746,0.796807,0.489874,0.590721,0.629865,0.0465461,0.851351,0.150959,0.234854,1.73945,0.170101,0.354732,0.818148,0.233219,0.369737,0.242389,0.202067,0.522822,0.235149,0.0349618,0.0937035,1.14148,0.0919402,0.241614,0.272549,0.167043,0.640469,0.190375,0.323893,0.728968,0.0859613,0.15988,0.301272,0.603923,0.292932,0.369939,0.366671,0.310813,0.167715,0.592653,0.734926,0.293507,0.757014,0.267557,0.0979814,0.266768,0.559896,0.303183,0.423107,0.465305,0.317765,0.4351,1.91534,1.17567,0.513487,1.01727,0.181085,0.200127,0.0128276,0.73304,0.0326098,0.118275,0.104456,0.450429,0.510572,0.165891,0.157528,0.464358,0.851126,0.0530449,0.684728,0.000729711,0.00893619,0.021314,0.38876,1.27332,0.90828,0.659533,0.537982,1.3492,0.738776,0.263897,0.975959,0.576706,0.392699,0.0172468,0.976012,0.532876,0.571612,0.493139,0.425079,0.214722,0.479058,0.288402,0.507144,0.104263,0.450084,0.569087,0.136085,0.225069,0.862131,2.77716,0.0757057,0.201199,0.433061,0.24923,0.725237,0.386689,0.23864,0.326716,0.968805,0.451097,0.295287,0.542501,0.765493,0.561324,0.660176,0.5898,0.779127,0.323981,0.920697,0.0869056,0.19775,0.659417,0.879842,1.7239,1.32497,0.844052,2.23307,0.573485,0.426604,0.260955,0.412168,1.56567,0.188015,0.0681329,0.145078,0.00407349,0.660531,0.047435,0.818076,1.04704,0.374997,0.699176,0.170141,0.150717,0.842888,0.643319,0.509866,0.464924,0.440625,0.316832,0.223866,0.299321,0.000933382
}}
}}

Revision as of 14:17, 26 November 2012


Full id: C528_Gingival_Mallassezderived_Keratinocyte_Sebocyte_Prostate_Urothelial_Small



Phase1 CAGE Peaks

Hg19::chr11:121421125..121421135,+p@chr11:121421125..121421135
+
Hg19::chr11:121421149..121421227,+p@chr11:121421149..121421227
+
Hg19::chr11:18154113..18154135,+p2@MRGPRX3
Hg19::chr11:93754513..93754538,+p1@HEPHL1
Hg19::chr12:28122899..28122916,-p2@PTHLH
Hg19::chr12:48883069..48883105,+p@chr12:48883069..48883105
+
Hg19::chr12:56333189..56333202,+p12@DGKA
Hg19::chr12:76653682..76653687,+p1@ENST00000553247
Hg19::chr13:30259714..30259730,+p@chr13:30259714..30259730
+
Hg19::chr13:30259768..30259777,+p@chr13:30259768..30259777
+
Hg19::chr18:67715292..67715310,-p4@RTTN
Hg19::chr1:30996257..30996268,+p@chr1:30996257..30996268
+
Hg19::chr20:21143565..21143577,+p@chr20:21143565..21143577
+
Hg19::chr5:52332019..52332031,-p@chr5:52332019..52332031
-
Hg19::chr6:29643393..29643442,-p@chr6:29643393..29643442
-
Hg19::chr8:123683812..123683837,-p@chr8:123683812..123683837
-
Hg19::chrX:43576227..43576231,+p@chrX:43576227..43576231
+


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
endo-epithelial cell1.14e-3742
general ecto-epithelial cell6.77e-3514
respiratory epithelial cell6.24e-2913
endodermal cell4.43e-2658
epithelial cell1.42e-22253
ecto-epithelial cell5.64e-1934
epithelial cell of Malassez9.60e-173
gingival epithelial cell1.38e-163
acinar cell4.14e-165
bronchial epithelial cell2.43e-153
epithelial cell of alimentary canal1.28e-1420
epidermal cell2.53e-149
stratified squamous epithelial cell6.43e-146
keratin accumulating cell6.43e-146
stratified epithelial cell6.43e-146
keratinizing barrier epithelial cell6.43e-146
epithelial fate stem cell6.43e-146
stratified epithelial stem cell6.43e-146
surface ectodermal cell6.43e-146
epithelial cell of tracheobronchial tree1.55e-139
epithelial cell of lower respiratory tract1.55e-139
protein secreting cell1.90e-136
embryonic cell2.41e-13250
mammary gland epithelial cell6.13e-124
transitional epithelial cell1.07e-114
urothelial cell1.07e-114
sebum secreting cell1.72e-112
epithelial cell of sweat gland1.72e-112
epithelial cell of skin gland1.72e-112
acinar cell of sebaceous gland1.72e-112
corneal epithelial cell2.09e-102
ectodermal cell3.04e-1072
keratinocyte6.12e-105
glandular epithelial cell5.35e-099
duct epithelial cell1.44e-073
branched duct epithelial cell1.44e-073
tracheal epithelial cell1.44e-073
tracheoblast1.44e-073
squamous epithelial cell1.99e-0763
epithelial cell of prostate2.42e-073
acinar cell of salivary gland3.45e-073
Uber Anatomy
Ontology termp-valuen
gingival epithelium1.38e-163
lower respiratory tract epithelium2.43e-153
epithelium of bronchus2.43e-153
surface structure5.61e-1499
jaw skeleton1.12e-124
splanchnocranium1.12e-124
mammary gland6.13e-124
mammary bud6.13e-124
mammary ridge6.13e-124
mammary placode6.13e-124
respiratory system1.22e-1174
skin gland1.72e-112
epidermis gland1.72e-112
gland of integumental system1.72e-112
sebaceous gland1.72e-112
skin sebaceous gland1.72e-112
sweat gland1.72e-112
sweat gland placode1.72e-112
sebaceous gland placode1.72e-112
head2.06e-1056
primary subdivision of cranial skeletal system3.15e-105
endoderm-derived structure9.75e-10160
endoderm9.75e-10160
presumptive endoderm9.75e-10160
mouth mucosa1.31e-0913
urothelium1.88e-095
bronchus2.11e-095
anterior region of body3.58e-0962
craniocervical region3.58e-0962
protuberance1.37e-086
pharyngeal arch1.37e-086
embryonic head1.37e-086
epithelial fold1.57e-0847
skin epidermis1.80e-0815
outer epithelium1.80e-0815
enveloping layer of ectoderm1.80e-0815
tracheobronchial tree5.11e-0815
lower respiratory tract5.11e-0815
transitional epithelium5.99e-086
oral opening1.34e-0722
orifice1.49e-0736
mouth1.65e-0729
stomodeum1.65e-0729
epithelial bud2.70e-0737
ectodermal placode5.43e-0731
exocrine gland5.54e-0731
exocrine system5.54e-0731


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

No analysis results for this cluster

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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