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Coexpression cluster:C3633: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3633_testicular_large_melanoma_papillary_osteosarcoma_Trabecular_gastric
|id=C3633
|ontology_enrichment_celltype=CL:0000066!1.17e-35!254;CL:0002321!5.12e-27!248;CL:0000220!4.06e-26!246;CL:0000548!3.73e-15!679;CL:0000004!3.73e-15!679;CL:0000255!3.73e-15!679;CL:0000012!2.51e-14!682;CL:0000222!5.39e-12!119;CL:0000076!2.93e-10!62;CL:0000223!1.06e-09!59;CL:0000071!1.67e-09!18;CL:0002546!1.67e-09!18;CL:0002139!1.95e-08!24;CL:0002078!5.10e-08!44;CL:0000055!1.20e-07!180;CL:0000115!2.12e-07!35;CL:0000003!2.15e-07!722;CL:0002076!3.61e-07!43;CL:0000213!5.92e-07!57;CL:0000215!5.92e-07!57
|ontology_enrichment_disease=DOID:305!1.94e-11!106;DOID:0050687!5.00e-10!143;DOID:14566!1.11e-09!239;DOID:162!1.86e-09!235
|ontology_enrichment_uberon=UBERON:0003914!9.75e-17!118;UBERON:0000490!2.55e-15!138;UBERON:0003104!1.52e-14!238;UBERON:0009142!1.52e-14!238;UBERON:0000119!2.24e-14!312;UBERON:0000483!1.39e-13!309;UBERON:0002049!2.89e-12!79;UBERON:0007798!2.89e-12!79;UBERON:0005256!4.24e-12!143;UBERON:0002100!9.19e-12!216;UBERON:0004119!9.28e-12!169;UBERON:0000925!9.28e-12!169;UBERON:0006595!9.28e-12!169;UBERON:0000481!1.06e-11!347;UBERON:0000055!1.61e-11!69;UBERON:0001048!3.03e-11!168;UBERON:0001981!7.88e-11!60;UBERON:0007500!7.88e-11!60;UBERON:0004537!7.88e-11!60;UBERON:0006965!7.88e-11!60;UBERON:0000466!3.87e-10!126;UBERON:0004872!6.44e-10!84;UBERON:0001637!1.62e-09!42;UBERON:0003509!1.62e-09!42;UBERON:0004572!1.62e-09!42;UBERON:0001986!1.67e-09!18;UBERON:0004638!1.67e-09!18;UBERON:0004852!1.67e-09!18;UBERON:0001007!3.66e-09!155;UBERON:0001555!3.66e-09!155;UBERON:0007026!3.66e-09!155;UBERON:0000487!3.93e-09!22;UBERON:0000077!4.71e-09!130;UBERON:0004111!1.06e-08!241;UBERON:0000477!1.18e-08!286;UBERON:0006914!2.74e-08!25;UBERON:0000464!6.12e-08!104;UBERON:0005911!8.29e-08!82;UBERON:0000486!1.04e-07!82;UBERON:0005177!1.40e-07!107;UBERON:0004535!1.46e-07!110;UBERON:0000475!2.14e-07!365;UBERON:0004573!6.46e-07!33;UBERON:0004571!6.46e-07!33;UBERON:0001009!6.86e-07!113
}}

Latest revision as of 12:30, 17 September 2013


Full id: C3633_testicular_large_melanoma_papillary_osteosarcoma_Trabecular_gastric



Phase1 CAGE Peaks

Hg19::chr17:41622834..41622883,-p6@ETV4
Hg19::chr17:41622901..41622913,-p16@ETV4
Hg19::chr17:41622925..41622976,-p3@ETV4


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
epithelial tube2.74e-16117
unilaminar epithelium7.18e-16148
organism subdivision1.48e-15264
cell layer5.07e-13309
epithelium2.31e-12306
trunk7.72e-12199
vasculature1.85e-1178
vascular system1.85e-1178
vessel8.43e-1168
anatomical cluster2.89e-10373
epithelial tube open at both ends5.16e-1059
blood vessel5.16e-1059
blood vasculature5.16e-1059
vascular cord5.16e-1059
trunk region element2.02e-09101
mesenchyme2.94e-09160
entire embryonic mesenchyme2.94e-09160
endoderm-derived structure3.14e-09160
endoderm3.14e-09160
presumptive endoderm3.14e-09160
trunk mesenchyme4.12e-09122
splanchnic layer of lateral plate mesoderm8.76e-0983
artery1.51e-0842
arterial blood vessel1.51e-0842
arterial system1.51e-0842
blood vessel endothelium1.54e-0818
endothelium1.54e-0818
cardiovascular system endothelium1.54e-0818
simple squamous epithelium2.11e-0822
primordium2.73e-08160
anatomical conduit3.78e-08240
multi-tissue structure4.01e-08342
immaterial anatomical entity4.31e-08117
squamous epithelium1.07e-0725
multilaminar epithelium1.80e-0783
endo-epithelium1.97e-0782
digestive system3.82e-07145
digestive tract3.82e-07145
primitive gut3.82e-07145
cardiovascular system6.38e-07109
Disease
Ontology termp-valuen
carcinoma3.32e-11106
cell type cancer6.60e-10143
disease of cellular proliferation3.58e-09239
cancer7.25e-09235


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.99448
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.19.66582
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.13.72456
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.97249
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.14.77883
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.214.6003
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



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
BHLHE40#8553344.87181354697741.10603738662898e-050.000284305780512292
CCNT2#90536.336201576962630.003930750035764890.0189819948668446
CHD2#1106310.34402283411690.0009033701102746880.00659908169175199
CTCF#1066435.360256373075030.0064925092527670.027913353114183
E2F1#186934.907389214879320.008460985347239390.0324885785756952
E2F6#187635.017155731697390.00791769806886330.0321682279862294
EGR1#195834.988179094810140.008056488137383440.032020838169509
ELF1#199734.258097958807540.01295179875054610.0461694624106862
EP300#203336.77394172622320.003216880500103790.0167314632744193
FOSL2#2355316.93020060456170.0002060162053171620.00242736083789701
FOXA1#3169311.08141974938550.000734755275698670.00580725792634277
GABPB1#255337.067683836182170.002832212825417420.0153938836988691
HDAC2#3066313.41562023662630.0004140761399857210.00390833239800892
HNF4A#3172323.13229036295378.07584663437677e-050.00122716913523596
HNF4G#3174328.75342252644684.20470658818262e-050.000756217240163948
RXRA#6256320.07461713913330.0001235730348432220.0016514196015344
SIN3A#2594235.408884726815140.006318961977991520.0276313042212132
SP1#666735.69838137814090.005403962701712170.0246198072153253
TCF7L2#6934310.77017656313730.0008003181298398380.00612878905721828
YY1#752834.911170749853860.008441455341808260.0328924804851365
ZBTB7A#5134137.35190930787590.002516255860282270.013998574857083



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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