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{{Coexpression_clusters
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|full_id=C4740_granulosa_caudate_putamen_occipital_neuroepithelioma_stomach_Hepatocyte
|id=C4740
|ontology_enrichment_celltype=CL:0000055!5.84e-10!180;CL:0000187!6.72e-07!54
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!2.88e-22!347;UBERON:0000483!4.44e-22!309;UBERON:0000119!1.08e-21!312;UBERON:0000475!7.42e-21!365;UBERON:0000468!6.34e-19!659;UBERON:0000922!2.75e-18!612;UBERON:0004111!1.28e-17!241;UBERON:0000073!1.90e-17!94;UBERON:0001016!1.90e-17!94;UBERON:0000467!2.00e-17!625;UBERON:0002050!2.09e-17!605;UBERON:0005423!2.09e-17!605;UBERON:0000923!2.81e-17!604;UBERON:0005291!2.81e-17!604;UBERON:0006598!2.81e-17!604;UBERON:0002532!2.81e-17!604;UBERON:0000480!4.86e-17!626;UBERON:0000025!6.66e-17!194;UBERON:0000477!2.91e-16!286;UBERON:0005743!1.09e-14!86;UBERON:0001017!1.50e-14!82;UBERON:0000955!3.97e-14!69;UBERON:0006238!3.97e-14!69;UBERON:0000924!5.42e-14!173;UBERON:0006601!5.42e-14!173;UBERON:0000033!1.76e-13!123;UBERON:0004121!2.29e-13!169;UBERON:0000153!1.77e-12!129;UBERON:0007811!1.77e-12!129;UBERON:0002346!5.19e-12!90;UBERON:0002616!1.15e-11!59;UBERON:0001049!2.05e-11!57;UBERON:0005068!2.05e-11!57;UBERON:0006241!2.05e-11!57;UBERON:0007135!2.05e-11!57;UBERON:0003075!2.12e-11!86;UBERON:0007284!2.12e-11!86;UBERON:0003056!1.19e-10!61;UBERON:0000062!2.07e-10!511;UBERON:0002780!5.96e-10!41;UBERON:0001890!5.96e-10!41;UBERON:0006240!5.96e-10!41;UBERON:0002020!6.53e-10!34;UBERON:0003528!6.53e-10!34;UBERON:0002791!6.68e-10!33;UBERON:0001893!7.10e-10!34;UBERON:0003080!9.23e-10!42;UBERON:0001869!1.37e-09!32;UBERON:0001048!6.29e-09!168;UBERON:0000490!4.54e-07!138;UBERON:0000956!5.10e-07!25;UBERON:0000203!5.10e-07!25;UBERON:0005256!8.89e-07!143
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4740_granulosa_caudate_putamen_occipital_neuroepithelioma_stomach_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr8:18871159..18871201,-p3@PSD3
Hg19::chr8:18871203..18871275,-p1@PSD3
Hg19::chr8:18871287..18871316,-p5@PSD3


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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell3.47e-08106
muscle cell8.39e-0755
Uber Anatomy
Ontology termp-valuen
anatomical cluster3.31e-25373
epithelium1.38e-23306
cell layer4.51e-23309
multi-tissue structure2.46e-22342
organ system subdivision1.05e-19223
multi-cellular organism1.20e-18656
anatomical system1.05e-17624
nervous system2.23e-1789
anatomical group2.43e-17625
anatomical conduit3.02e-17240
embryo4.25e-17592
tube8.95e-17192
embryonic structure7.41e-16564
germ layer1.32e-15560
germ layer / neural crest1.32e-15560
embryonic tissue1.32e-15560
presumptive structure1.32e-15560
germ layer / neural crest derived structure1.32e-15560
epiblast (generic)1.32e-15560
ectoderm-derived structure4.05e-15171
ectoderm4.05e-15171
presumptive ectoderm4.05e-15171
developing anatomical structure1.23e-14581
central nervous system1.26e-1481
brain2.36e-1468
future brain2.36e-1468
neurectoderm2.85e-1486
structure with developmental contribution from neural crest5.80e-14132
neural plate1.14e-1382
presumptive neural plate1.14e-1382
neural tube9.48e-1256
neural rod9.48e-1256
future spinal cord9.48e-1256
neural keel9.48e-1256
regional part of nervous system2.18e-1153
regional part of brain2.18e-1153
ecto-epithelium5.27e-11104
pre-chordal neural plate9.48e-1161
organ2.24e-10503
regional part of forebrain5.14e-1041
forebrain5.14e-1041
anterior neural tube5.14e-1041
future forebrain5.14e-1041
brain grey matter6.92e-1034
gray matter6.92e-1034
telencephalon8.04e-1034
regional part of telencephalon1.19e-0932
cerebral hemisphere1.55e-0932
primordium6.58e-08160
organism subdivision7.64e-08264
trunk mesenchyme3.63e-07122
cerebral cortex5.64e-0725
pallium5.64e-0725
unilaminar epithelium9.62e-07148


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)
MA0003.112.1872
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
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
MA0050.11.90116
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
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
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0105.10.31555
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
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.94723
MA0146.19.01037
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.21.34467
MA0065.22.97249
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.16.1256
MA0163.110.4767
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.213.0679
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
CTCF#1066435.360256373075030.0064925092527670.0281450761186175
CTCFL#140690319.74647435897440.0001298372005551160.00172388347174877
E2F1#186934.907389214879320.008460985347239390.0327899680389007
E2F6#187635.017155731697390.00791769806886330.0324497299617005
MAX#414936.452555509007120.003721913834265510.0187467064835715
RAD21#5885310.35503389545630.0009004912073565420.00668940900527135
SMC3#9126315.04493284493280.0002935825420371870.00310968226245656
TAF7#6879311.43306940492390.0006690181981945830.00545957115183967
TFAP2A#7020316.5186343730450.0002218033880766340.00249595130345174
TFAP2C#7022310.80922860986020.0007916746575753130.00619153134360552



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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