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Coexpression cluster:C4725: Difference between revisions

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|ontology_enrichment_disease=DOID:305!8.53e-19!106;DOID:0050687!1.38e-12!143;DOID:162!1.06e-10!235;DOID:14566!5.90e-10!239;DOID:1749!9.47e-09!14
|ontology_enrichment_disease=DOID:305!8.53e-19!106;DOID:0050687!1.38e-12!143;DOID:162!1.06e-10!235;DOID:14566!5.90e-10!239;DOID:1749!9.47e-09!14
|ontology_enrichment_uberon=UBERON:0004119!2.30e-22!169;UBERON:0000925!2.30e-22!169;UBERON:0006595!2.30e-22!169;UBERON:0001004!7.36e-20!72;UBERON:0000065!1.66e-19!53;UBERON:0001007!3.18e-16!155;UBERON:0001555!3.18e-16!155;UBERON:0007026!3.18e-16!155;UBERON:0008947!6.23e-16!38;UBERON:0003258!6.23e-16!38;UBERON:0000077!1.50e-15!130;UBERON:0000072!3.97e-15!46;UBERON:0004921!2.05e-13!129;UBERON:0004185!2.05e-13!129;UBERON:0005153!6.77e-12!37;UBERON:0001041!1.06e-11!98;UBERON:0005157!2.42e-10!51;UBERON:0005911!2.63e-10!82;UBERON:0005178!4.79e-10!34;UBERON:0002224!4.79e-10!34;UBERON:0000464!6.05e-10!104;UBERON:0005181!1.53e-09!35;UBERON:0005156!2.71e-09!59;UBERON:0000990!2.71e-09!59;UBERON:0000161!5.23e-09!35;UBERON:0001048!2.15e-08!168;UBERON:0005631!2.77e-08!14;UBERON:0000158!2.77e-08!14;UBERON:0001557!6.84e-08!19;UBERON:0001737!1.04e-07!9;UBERON:0002048!1.19e-07!22;UBERON:0000117!1.19e-07!22;UBERON:0000171!1.19e-07!22;UBERON:0000170!1.19e-07!22;UBERON:0005597!1.19e-07!22;UBERON:0000118!1.19e-07!22;UBERON:0004807!1.57e-07!28;UBERON:0000466!1.87e-07!126;UBERON:0003133!2.15e-07!48;UBERON:0004175!2.36e-07!25;UBERON:0003100!3.26e-07!41;UBERON:0000064!5.32e-07!219;UBERON:0007196!8.05e-07!14;UBERON:0001558!8.05e-07!14
|ontology_enrichment_uberon=UBERON:0004119!2.30e-22!169;UBERON:0000925!2.30e-22!169;UBERON:0006595!2.30e-22!169;UBERON:0001004!7.36e-20!72;UBERON:0000065!1.66e-19!53;UBERON:0001007!3.18e-16!155;UBERON:0001555!3.18e-16!155;UBERON:0007026!3.18e-16!155;UBERON:0008947!6.23e-16!38;UBERON:0003258!6.23e-16!38;UBERON:0000077!1.50e-15!130;UBERON:0000072!3.97e-15!46;UBERON:0004921!2.05e-13!129;UBERON:0004185!2.05e-13!129;UBERON:0005153!6.77e-12!37;UBERON:0001041!1.06e-11!98;UBERON:0005157!2.42e-10!51;UBERON:0005911!2.63e-10!82;UBERON:0005178!4.79e-10!34;UBERON:0002224!4.79e-10!34;UBERON:0000464!6.05e-10!104;UBERON:0005181!1.53e-09!35;UBERON:0005156!2.71e-09!59;UBERON:0000990!2.71e-09!59;UBERON:0000161!5.23e-09!35;UBERON:0001048!2.15e-08!168;UBERON:0005631!2.77e-08!14;UBERON:0000158!2.77e-08!14;UBERON:0001557!6.84e-08!19;UBERON:0001737!1.04e-07!9;UBERON:0002048!1.19e-07!22;UBERON:0000117!1.19e-07!22;UBERON:0000171!1.19e-07!22;UBERON:0000170!1.19e-07!22;UBERON:0005597!1.19e-07!22;UBERON:0000118!1.19e-07!22;UBERON:0004807!1.57e-07!28;UBERON:0000466!1.87e-07!126;UBERON:0003133!2.15e-07!48;UBERON:0004175!2.36e-07!25;UBERON:0003100!3.26e-07!41;UBERON:0000064!5.32e-07!219;UBERON:0007196!8.05e-07!14;UBERON:0001558!8.05e-07!14
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}}
}}

Revision as of 13:57, 5 September 2012


Full id: C4725_Corneal_Keratinocyte_mesothelioma_Bronchial_Urothelial_papillotubular_Gingival



Phase1 CAGE Peaks

Hg19::chr8:124194824..124194835,+p5@FAM83A
Hg19::chr8:124194875..124194920,+p2@FAM83A
Hg19::chr8:124194922..124194957,+p1@FAM83A


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.30e-22169
endoderm2.30e-22169
presumptive endoderm2.30e-22169
respiratory system7.36e-2072
respiratory tract1.66e-1953
digestive system3.18e-16155
digestive tract3.18e-16155
primitive gut3.18e-16155
respiratory primordium6.23e-1638
endoderm of foregut6.23e-1638
mixed endoderm/mesoderm-derived structure1.50e-15130
segment of respiratory tract3.97e-1546
subdivision of digestive tract2.05e-13129
endodermal part of digestive tract2.05e-13129
epithelial bud6.77e-1237
foregut1.06e-1198
epithelial fold2.42e-1051
endo-epithelium2.63e-1082
thoracic cavity element4.79e-1034
thoracic cavity4.79e-1034
anatomical space6.05e-10104
thoracic segment organ1.53e-0935
reproductive structure2.71e-0959
reproductive system2.71e-0959
orifice5.23e-0935
primordium2.15e-08168
extraembryonic membrane2.77e-0814
membranous layer2.77e-0814
upper respiratory tract6.84e-0819
larynx1.04e-079
lung1.19e-0722
respiratory tube1.19e-0722
respiration organ1.19e-0722
pair of lungs1.19e-0722
lung primordium1.19e-0722
lung bud1.19e-0722
respiratory system epithelium1.57e-0728
immaterial anatomical entity1.87e-07126
reproductive organ2.15e-0748
internal genitalia2.36e-0725
female organism3.26e-0741
organ part5.32e-07219
tracheobronchial tree8.05e-0714
lower respiratory tract8.05e-0714
Disease
Ontology termp-valuen
carcinoma8.53e-19106
cell type cancer1.38e-12143
cancer1.06e-10235
disease of cellular proliferation5.90e-10239
squamous cell carcinoma9.47e-0914


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
CCNT2#90536.336201576962630.003930750035764890.0191225825873509
CEBPB#105137.971147625824820.001974187055288560.0115826145647594
CHD2#1106310.34402283411690.0009033701102746880.0066296866662201
E2F1#186934.907389214879320.008460985347239390.0327851017949889
E2F4#1874312.66806031528440.0004917987006298980.00439037221088007
E2F6#187635.017155731697390.00791769806886330.0324446372116771
EP300#203336.77394172622320.003216880500103790.016853161903704
FOS#235338.99795530889440.001372499272417130.00902092205865151
FOXA1#3169311.08141974938550.000734755275698670.00584307517236681
GATA1#2623313.56030814380040.0004009615963782630.00389544448038599
GATA2#2624312.7449317335540.0004829527704283790.00439059056326336
GATA3#2625327.2365163572064.94721007899563e-050.00085500856104621
GTF2F1#2962312.73966087675770.0004835525047438590.00436074087237233
HDAC2#3066313.41562023662630.0004140761399857210.00393643710030664
HMGN3#932438.178547723350590.001827766942164210.0109261148001081
JUN#3725312.51282919233630.0005103313992726250.00446498291100224
JUNB#3726330.61063265982113.4847716247536e-050.000682953769408222
JUND#372736.994663941871030.002921845042734990.0157718924135931
MAX#414936.452555509007120.003721913834265510.0187458024178653
MXI1#460139.96157162875930.001011470541259020.00723590464131454
MYC#460935.22228187160940.007020843755740150.0296166855564159
RAD21#5885310.35503389545630.0009004912073565420.00668893322938192
RFX5#5993312.04791082719510.0005717246050312580.00486914670348688
SMARCA4#65973156.7659033078882.58908533335753e-071.34194284432023e-05
SMARCB1#6598318.25271578115740.000164397760679890.00204131943022792
SMARCC1#6599343.66335931963151.20046018043203e-050.000302691600154855
SMARCC2#6601394.15537442689761.19621075407887e-064.86870829872342e-05
SMC3#9126315.04493284493280.0002935825420371870.00310936691084289
STAT1#6772320.70658749719920.0001125992441046670.00155387849564578
STAT2#6773365.26377118644073.59360517547754e-060.000118619636827338
STAT3#6774310.51946499715420.0008589184530415310.0064568188524584
TAL1#6886329.86861667744023.75103522793067e-050.000722927418656304
TFAP2A#7020316.5186343730450.0002218033880766340.00249514477028604
TFAP2C#7022310.80922860986020.0007916746575753130.0061901407174147
YY1#752834.911170749853860.008441455341808260.0331360277547588



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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