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Coexpression cluster:C3276: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3276_testicular_oral_pancreatic_H9_migratory_small_merkel
|id=C3276
}}

Latest revision as of 12:22, 17 September 2013


Full id: C3276_testicular_oral_pancreatic_H9_migratory_small_merkel



Phase1 CAGE Peaks

Hg19::chr12:31479045..31479074,-p2@FAM60A
Hg19::chr12:31479076..31479092,-p1@FAM60A
Hg19::chr12:31479107..31479142,-p3@FAM60A


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell1.70e-17253
lymphocyte2.72e-1653
common lymphoid progenitor2.72e-1653
lymphoid lineage restricted progenitor cell6.30e-1652
nucleate cell7.88e-1555
lymphocyte of B lineage1.29e-1124
pro-B cell1.29e-1124
endo-epithelial cell4.38e-0842
endodermal cell1.38e-0758
B cell2.00e-0714
Disease
Ontology termp-valuen
cancer1.50e-40235
disease of cellular proliferation1.12e-39239
cell type cancer4.61e-26143
carcinoma6.63e-25106
organ system cancer4.49e-21137
hematologic cancer1.22e-1251
immune system cancer1.22e-1251
leukemia1.22e-0939
germ cell and embryonal cancer4.36e-0922
germ cell cancer4.36e-0922
myeloid leukemia4.53e-0731
squamous cell carcinoma9.51e-0714


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
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.12.72668
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.12.74347
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.11.97353
MA0042.11.89908
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.12.15619
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
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
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.12.19699
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
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
MA0131.13.943
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.12.29531
MA0144.11.31729
MA0145.10.273764
MA0146.11.70974
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.23.15214
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
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
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.10519
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
BCLAF1#9774321.65264761012189.8473954032885e-050.00138961238822328
CCNT2#90536.336201576962630.003930750035764890.018942580425676
E2F1#186934.907389214879320.008460985347239390.0324051798261885
E2F4#1874312.66806031528440.0004917987006298980.00436055390908277
E2F6#187635.017155731697390.00791769806886330.0320895831663632
EGR1#195834.988179094810140.008056488137383440.0319454635551915
ELF1#199734.258097958807540.01295179875054610.046056278846043
ETS1#211339.728760922202340.001085840092584840.00760590566260682
FOXA1#3169311.08141974938550.000734755275698670.00579891983969571
GATA1#2623313.56030814380040.0004009615963782630.00387131627661546
GTF2B#2959331.94382993432423.06634405746243e-050.000626214131828938
GTF2F1#2962312.73966087675770.0004835525047438590.00432933905211692
HDAC2#3066313.41562023662630.0004140761399857210.00390128082850417
HMGN3#932438.178547723350590.001827766942164210.0108429509612433
MAX#414936.452555509007120.003721913834265510.0185987061692275
MYC#460935.22228187160940.007020843755740150.0293476046029916
NANOG#79923329.24477848101273.99627955670032e-050.00073506065625612
NFKB1#479035.488063424193840.006049381815655430.0268847398912867
NRF1#4899312.21027944771090.0005492172401020010.00469968859803465
POU2F2#545239.106124057742520.001324165192682130.00880239886439622
REST#597839.650028716128020.001112636247114590.00765750359225045
RFX5#5993312.04791082719510.0005717246050312580.00483445437817663
SIN3A#2594235.408884726815140.006318961977991520.0275724282439714
SRF#6722313.79717826216780.0003806615025800190.00374102819873479
TAF7#6879311.43306940492390.0006690181981945830.00541094955480865
TCF12#6938310.63446490218640.0008313523990202070.00628124236426762
YY1#752834.911170749853860.008441455341808260.0328287899625065
ZBTB7A#5134137.35190930787590.002516255860282270.0139754970108498
ZNF263#1012738.221841637010680.001799043925565870.0109004089193116



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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