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{{Coexpression_clusters
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|full_id=C3194_Renal_pleomorphic_Alveolar_Mesenchymal_Osteoblast_gastric_glioma
|id=C3194
|ontology_enrichment_celltype=CL:0000220!4.07e-20!246;CL:0002321!4.38e-20!248;CL:0000066!1.66e-18!254;CL:0000548!7.75e-13!679;CL:0000004!7.75e-13!679;CL:0000255!7.75e-13!679;CL:0000222!1.68e-12!119;CL:0000012!3.29e-12!682;CL:0002371!5.35e-11!591;CL:0000003!3.30e-10!722;CL:1000497!2.15e-09!18;CL:0002518!2.15e-09!18;CL:0000144!2.67e-09!625;CL:0000183!5.91e-09!59;CL:1000449!6.42e-09!16;CL:0000359!1.98e-08!32;CL:0000115!2.63e-08!35;CL:0002078!2.73e-08!44;CL:0000192!5.12e-08!42;CL:0000514!5.12e-08!42;CL:0000055!5.89e-08!180;CL:0002681!4.33e-07!13;CL:0002584!4.33e-07!13;CL:0000187!5.34e-07!54;CL:0002139!8.02e-07!24;CL:0000071!9.74e-07!18;CL:0002546!9.74e-07!18
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!1.10e-22!118;UBERON:0002100!2.07e-16!216;UBERON:0002049!9.10e-15!79;UBERON:0007798!9.10e-15!79;UBERON:0005256!1.24e-14!143;UBERON:0004872!1.85e-14!84;UBERON:0001009!2.61e-14!113;UBERON:0000055!5.00e-14!69;UBERON:0009569!1.21e-13!113;UBERON:0004535!1.95e-13!110;UBERON:0001981!8.28e-13!60;UBERON:0007500!8.28e-13!60;UBERON:0004537!8.28e-13!60;UBERON:0006965!8.28e-13!60;UBERON:0000490!1.04e-12!138;UBERON:0003104!4.88e-12!238;UBERON:0009142!4.88e-12!238;UBERON:0001637!8.84e-11!42;UBERON:0003509!8.84e-11!42;UBERON:0004572!8.84e-11!42;UBERON:0000119!6.06e-10!312;UBERON:0000477!8.13e-10!286;UBERON:0004111!8.86e-10!241;UBERON:0000483!2.19e-09!309;UBERON:0000080!3.39e-09!18;UBERON:0002120!3.39e-09!18;UBERON:0004875!3.39e-09!18;UBERON:0005721!3.39e-09!18;UBERON:0005754!3.39e-09!18;UBERON:0007297!3.39e-09!18;UBERON:0001008!5.12e-09!45;UBERON:0006554!5.88e-09!44;UBERON:0006555!5.90e-09!17;UBERON:0005103!5.90e-09!17;UBERON:0000083!5.90e-09!17;UBERON:0009201!5.90e-09!17;UBERON:0004819!5.90e-09!17;UBERON:0006553!5.90e-09!17;UBERON:0003074!5.90e-09!17;UBERON:0003060!5.90e-09!17;UBERON:0004211!6.42e-09!16;UBERON:0001285!6.42e-09!16;UBERON:0007684!6.42e-09!16;UBERON:0003220!6.42e-09!16;UBERON:0004208!6.42e-09!16;UBERON:0002417!7.55e-09!61;UBERON:0000916!7.55e-09!61;UBERON:0003064!8.71e-09!37;UBERON:0003103!1.39e-08!69;UBERON:0004876!3.61e-08!20;UBERON:0005172!7.32e-08!55;UBERON:0005173!7.32e-08!55;UBERON:0000466!8.34e-08!126;UBERON:0000058!1.60e-07!26;UBERON:0003887!1.65e-07!21;UBERON:0000025!1.88e-07!194;UBERON:0000481!2.16e-07!347;UBERON:0004573!3.03e-07!33;UBERON:0004571!3.03e-07!33;UBERON:0000353!3.39e-07!17;UBERON:0001851!3.98e-07!16;UBERON:0005177!4.23e-07!107;UBERON:0001225!4.33e-07!13;UBERON:0008987!4.33e-07!13;UBERON:0000487!4.43e-07!22;UBERON:0000475!9.24e-07!365;UBERON:0001986!9.74e-07!18;UBERON:0004638!9.74e-07!18;UBERON:0004852!9.74e-07!18
}}

Latest revision as of 12:21, 17 September 2013


Full id: C3194_Renal_pleomorphic_Alveolar_Mesenchymal_Osteoblast_gastric_glioma



Phase1 CAGE Peaks

Hg19::chr11:67275542..67275556,-p4@CDK2AP2
Hg19::chr11:67275568..67275585,-p5@CDK2AP2
Hg19::chr11:67275590..67275616,-p3@CDK2AP2


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
epithelial tube4.93e-22117
trunk4.45e-18199
organism subdivision2.66e-16264
vasculature1.09e-1478
vascular system1.09e-1478
splanchnic layer of lateral plate mesoderm2.65e-1483
circulatory system6.44e-14112
subdivision of trunk6.57e-14112
vessel6.79e-1468
cardiovascular system3.70e-13109
unilaminar epithelium1.57e-12148
epithelial tube open at both ends1.79e-1259
blood vessel1.79e-1259
blood vasculature1.79e-1259
vascular cord1.79e-1259
mesenchyme3.71e-12160
entire embryonic mesenchyme3.71e-12160
trunk mesenchyme2.33e-11122
artery1.25e-1042
arterial blood vessel1.25e-1042
arterial system1.25e-1042
nephron epithelium2.88e-1015
renal tubule2.88e-1015
nephron tubule2.88e-1015
nephron2.88e-1015
uriniferous tubule2.88e-1015
nephrogenic mesenchyme2.88e-1015
renal system2.90e-1048
excretory tube4.23e-1016
kidney epithelium4.23e-1016
urinary system structure4.68e-1047
anatomical conduit2.65e-09240
cell layer6.57e-09309
anatomical cluster8.51e-09373
compound organ1.12e-0868
cortex of kidney1.78e-0812
renal parenchyma1.78e-0812
abdominal segment of trunk2.04e-0860
abdomen2.04e-0860
parenchyma2.20e-0815
epithelium2.30e-08306
cortex2.50e-0815
epithelial vesicle3.77e-0878
trunk region element4.00e-08101
abdomen element1.81e-0754
abdominal segment element1.81e-0754
multi-tissue structure2.28e-07342
nephron tubule epithelium3.03e-0710
simple squamous epithelium3.52e-0722
systemic artery3.65e-0733
systemic arterial system3.65e-0733
kidney5.04e-0726
kidney mesenchyme5.04e-0726
upper urinary tract5.04e-0726
kidney rudiment5.04e-0726
kidney field5.04e-0726
tube6.26e-07192


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.12.16573
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.113.7629
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.13.60951
MA0101.10.646932
MA0103.11.52002
MA0105.10.846801
MA0106.13.70241
MA0107.11.36919
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
MA0131.11.06461
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
MA0145.13.85295
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.24.02533
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
CCNT2#90536.336201576962630.003930750035764890.0189268604419202
CHD2#1106310.34402283411690.0009033701102746880.00658618296313984
E2F1#186934.907389214879320.008460985347239390.0323838035943979
E2F4#1874312.66806031528440.0004917987006298980.00435796406712082
E2F6#187635.017155731697390.00791769806886330.0320659403061119
ELF1#199734.258097958807540.01295179875054610.0460296358834955
ELK4#2005316.2356816584680.0002336043955745990.00255096293072099
ETS1#211339.728760922202340.001085840092584840.00760233649054553
FOS#235338.99795530889440.001372499272417130.00895051211439104
FOXA1#3169311.08141974938550.000734755275698670.00579716750311198
FOXA2#3170324.63046375266526.68983856509345e-050.0010704459168068
GABPB1#255337.067683836182170.002832212825417420.0153674914419041
GATA1#2623313.56030814380040.0004009615963782630.00386988523834668
IRF1#365937.63716375356390.002244692747297240.012768011864004
IRF3#3661346.98195221148969.63568551583244e-060.000253167637632207
MXI1#460139.96157162875930.001011470541259020.00718521098208074
NANOG#79923329.24477848101273.99627955670032e-050.000734284730158735
NFKB1#479035.488063424193840.006049381815655430.0268687329865288
NFYA#4800318.42558069983050.0001598135507814160.00199078809995949
NFYB#4801316.75979325353650.0002123649923296180.00245046817300994
PBX3#5090321.91451268674419.49854535978121e-050.00136154073405187
RFX5#5993312.04791082719510.0005717246050312580.00483249805963577
SP1#666735.69838137814090.005403962701712170.0245566053432588
SP2#6668326.15353049384465.58768218891694e-050.000937916972240913
USF1#739136.361499277207960.00388404057290560.0189607045617317



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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