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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:45, 17 September 2013


Full id: C1461_medulla_locus_globus_spinal_mesothelioma_kidney_testicular



Phase1 CAGE Peaks

Hg19::chr1:110546475..110546482,+p27@AHCYL1
Hg19::chr1:110546552..110546575,+p7@AHCYL1
Hg19::chr1:110546650..110546663,+p12@AHCYL1
Hg19::chr1:110546674..110546695,+p5@AHCYL1
Hg19::chr1:110546700..110546758,+p2@AHCYL1
Hg19::chr1:110546760..110546769,+p21@AHCYL1


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>

Cell Type
Ontology termp-valuen
germ line cell1.33e-087
germ cell1.33e-087
Uber Anatomy
Ontology termp-valuen
neural tube4.31e-2356
neural rod4.31e-2356
future spinal cord4.31e-2356
neural keel4.31e-2356
adult organism8.78e-23114
regional part of nervous system7.54e-2253
regional part of brain7.54e-2253
regional part of forebrain5.03e-1941
forebrain5.03e-1941
anterior neural tube5.03e-1941
future forebrain5.03e-1941
brain2.17e-1868
future brain2.17e-1868
central nervous system3.52e-1681
organ system subdivision1.92e-15223
brain grey matter1.70e-1434
gray matter1.70e-1434
tube2.57e-14192
telencephalon5.73e-1434
nervous system1.14e-1389
neural plate4.34e-1382
presumptive neural plate4.34e-1382
regional part of telencephalon1.19e-1232
neurectoderm1.58e-1286
cerebral hemisphere3.14e-1232
pre-chordal neural plate3.24e-1161
neural nucleus4.04e-119
nucleus of brain4.04e-119
basal ganglion1.05e-109
nuclear complex of neuraxis1.05e-109
aggregate regional part of brain1.05e-109
collection of basal ganglia1.05e-109
cerebral subcortex1.05e-109
anatomical conduit2.08e-10240
anatomical cluster4.29e-09373
telencephalic nucleus7.06e-097
ecto-epithelium1.32e-08104
regional part of cerebral cortex1.38e-0822
brainstem3.88e-086
multi-tissue structure5.77e-08342
cerebral cortex5.06e-0725
pallium5.06e-0725
neocortex5.15e-0720
diencephalon5.50e-077
future diencephalon5.50e-077
Disease
Ontology termp-valuen
carcinoma1.12e-20106
cell type cancer2.13e-16143
cancer1.68e-10235
disease of cellular proliferation3.74e-10239


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.14.79234
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.13.76196
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.13.9816
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.14.65546
MA0143.10.725558
MA0144.13.11622
MA0145.10.107156
MA0146.10.232472
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.23.82234
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.354331
MA0150.14.22814
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.22.58359
MA0079.25.9246e-06
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
BATF#10538416.23853452820243.98325915717398e-050.00074247296647527
CEBPB#105167.971147625824823.89609159898068e-060.000126998723628571
EP300#203366.77394172622321.03454107484288e-050.000269711521007278
ESR1#2099630.76860329615451.17571957705476e-091.07616982390905e-07
FOS#235368.99795530889441.88302066097805e-066.94178590935003e-05
GATA2#2624612.7449317335542.33109997620343e-071.22710559684833e-05
GATA3#2625418.15767757147072.56597141799789e-050.000554839521582363
GTF2F1#2962612.73966087675772.33689372527042e-071.22891663531479e-05
JUN#3725612.51282919233632.60292147666678e-071.34577483218615e-05
JUNB#3726630.61063265982111.2126128927106e-091.10702865298778e-07
JUND#372766.994663941871038.53468650061654e-060.000232244430286058
MAFF#23764656.31535648994523.12096011318554e-113.59768160332213e-09
MAFK#7975627.10073313782992.5187992661962e-092.12832424403127e-07
MXI1#460158.301309690632755.60234779909565e-050.000939472706791507
NFE2#4778677.2042606516294.69314969603843e-126.15763644603716e-10
NFKB1#479054.57338618682820.00102196259371130.00724594374233633
POLR2A#543062.147453176558070.01019570676818780.0380377730643269
SMARCB1#6598412.16847718743830.0001234985463193470.00166062375164752
SMARCC1#6599429.10890621308763.97173589497568e-060.000128382582833601
STAT1#6772620.70658749719921.2666425711927e-089.38870713220686e-07
STAT3#6774610.51946499715427.37398960627247e-073.26742511875049e-05
TAF1#687263.343046285745290.0007162474284635620.00573255921383294
TBP#690863.706770687096390.000385416472907960.00377815947193866
TFAP2A#7020616.5186343730454.91595718330683e-083.15949324472235e-06
TFAP2C#7022610.80922860986026.2644941908553e-072.86452499474053e-05
TRIM28#10155618.59052504526252.41896703530258e-081.69326071179602e-06
ZNF263#1012768.221841637010683.23542093046082e-060.000108755753639008



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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