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{{Coexpression_clusters
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matrix!0.00309078064288237!11001$GO:0000038!very-long-chain fatty acid metabolic process!0.00309078064288237!11001$GO:0004467!long-chain-fatty-acid-CoA ligase activity!0.00309078064288237!11001$GO:0015645!fatty-acid ligase activity!0.00309078064288237!11001$GO:0016877!ligase activity, forming carbon-sulfur bonds!0.00645629734290984!11001$GO:0031903!microbody membrane!0.00645629734290984!11001$GO:0005778!peroxisomal membrane!0.00645629734290984!11001$GO:0044439!peroxisomal part!0.00645629734290984!11001$GO:0044438!microbody part!0.00645629734290984!11001$GO:0042579!microbody!0.0112392023377541!11001$GO:0005777!peroxisome!0.0112392023377541!11001$GO:0006631!fatty acid metabolic process!0.0196779700930178!11001$GO:0032787!monocarboxylic acid metabolic process!0.0272939706002228!11001$GO:0005789!endoplasmic reticulum membrane!0.0384905216060285!11001$GO:0042175!nuclear envelope-endoplasmic reticulum network!0.0384905216060285!11001$GO:0044432!endoplasmic reticulum 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|full_id=C3496_liver_Hepatocyte_epitheloid_hairy_cord_cervical_non
|gostat_on_coexpression_clusters=GO:0005782!peroxisomal matrix!0.00309078064288237!11001$GO:0000038!very-long-chain fatty acid metabolic process!0.00309078064288237!11001$GO:0004467!long-chain-fatty-acid-CoA ligase activity!0.00309078064288237!11001$GO:0015645!fatty-acid ligase activity!0.00309078064288237!11001$GO:0016877!ligase activity, forming carbon-sulfur bonds!0.00645629734290984!11001$GO:0031903!microbody membrane!0.00645629734290984!11001$GO:0005778!peroxisomal membrane!0.00645629734290984!11001$GO:0044439!peroxisomal part!0.00645629734290984!11001$GO:0044438!microbody part!0.00645629734290984!11001$GO:0042579!microbody!0.0112392023377541!11001$GO:0005777!peroxisome!0.0112392023377541!11001$GO:0006631!fatty acid metabolic process!0.0196779700930178!11001$GO:0032787!monocarboxylic acid metabolic process!0.0272939706002228!11001$GO:0005789!endoplasmic reticulum membrane!0.0384905216060285!11001$GO:0042175!nuclear envelope-endoplasmic reticulum network!0.0384905216060285!11001$GO:0044432!endoplasmic reticulum part!0.0401801483574708!11001$GO:0016874!ligase activity!0.0470525900222328!11001$GO:0044255!cellular lipid metabolic process!0.0493288590604027!11001$GO:0019752!carboxylic acid metabolic process!0.0493288590604027!11001$GO:0006082!organic acid metabolic process!0.0493288590604027!11001
|id=C3496
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:162!5.02e-23!235;DOID:14566!9.57e-22!239;DOID:305!3.62e-19!106;DOID:0050687!1.22e-13!143;DOID:8692!3.62e-13!31;DOID:1240!4.95e-13!39;DOID:0050686!3.00e-11!137;DOID:2531!3.02e-09!51;DOID:0060083!3.02e-09!51
|ontology_enrichment_uberon=UBERON:0004921!9.01e-12!129;UBERON:0004185!9.01e-12!129;UBERON:0007023!6.57e-11!115;UBERON:0001007!1.22e-09!155;UBERON:0001555!1.22e-09!155;UBERON:0007026!1.22e-09!155;UBERON:0008947!2.54e-09!38;UBERON:0003258!2.54e-09!38;UBERON:0000077!1.25e-08!130;UBERON:0001737!3.96e-08!9;UBERON:0001041!6.95e-08!98;UBERON:0004119!9.62e-08!169;UBERON:0000925!9.62e-08!169;UBERON:0006595!9.62e-08!169;UBERON:0000072!2.93e-07!46;UBERON:0005911!6.87e-07!82
}}

Latest revision as of 12:27, 17 September 2013


Full id: C3496_liver_Hepatocyte_epitheloid_hairy_cord_cervical_non



Phase1 CAGE Peaks

Hg19::chr15:50474385..50474404,+p2@SLC27A2
Hg19::chr15:50474553..50474562,+p4@SLC27A2
Hg19::chr15:50474813..50474866,+p1@CU691220


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

GO IDGO nameFDR corrected p-value
GO:0005782peroxisomal matrix0.00309078064288237
GO:0000038very-long-chain fatty acid metabolic process0.00309078064288237
GO:0004467long-chain-fatty-acid-CoA ligase activity0.00309078064288237
GO:0015645fatty-acid ligase activity0.00309078064288237
GO:0016877ligase activity, forming carbon-sulfur bonds0.00645629734290984
GO:0031903microbody membrane0.00645629734290984
GO:0005778peroxisomal membrane0.00645629734290984
GO:0044439peroxisomal part0.00645629734290984
GO:0044438microbody part0.00645629734290984
GO:0042579microbody0.0112392023377541
GO:0005777peroxisome0.0112392023377541
GO:0006631fatty acid metabolic process0.0196779700930178
GO:0032787monocarboxylic acid metabolic process0.0272939706002228
GO:0005789endoplasmic reticulum membrane0.0384905216060285
GO:0042175nuclear envelope-endoplasmic reticulum network0.0384905216060285
GO:0044432endoplasmic reticulum part0.0401801483574708
GO:0016874ligase activity0.0470525900222328
GO:0044255cellular lipid metabolic process0.0493288590604027
GO:0019752carboxylic acid metabolic process0.0493288590604027
GO:0006082organic acid metabolic process0.0493288590604027



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
larynx5.62e-119
subdivision of digestive tract1.49e-10118
organ system subdivision3.37e-09223
digestive system1.97e-07145
digestive tract1.97e-07145
primitive gut1.97e-07145
foregut2.27e-0787
upper respiratory tract6.81e-0719
Disease
Ontology termp-valuen
cancer1.49e-17235
disease of cellular proliferation1.60e-16239
carcinoma4.79e-13106
leukemia1.32e-1139
organ system cancer7.41e-11137
myeloid leukemia9.15e-1131
hematologic cancer2.31e-0951
immune system cancer2.31e-0951
cell type cancer1.51e-08143


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)
MA0003.12.61626
MA0004.10.826076
MA0006.11.5435
MA0007.11.88666
MA0009.11.3275
MA0014.10.118426
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
MA0055.10.557638
MA0056.10
MA0057.10.333427
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
MA0073.10.0185922
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
MA0100.10.956299
MA0101.11.55947
MA0103.11.52002
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
MA0116.11.3784
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.752137
MA0146.10.107247
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.23.15214
MA0047.20.973066
MA0112.23.77966
MA0065.22.13692
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
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.14.42822
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#90536.336201576962630.003930750035764890.0189662094241279
CTBP2#1488362.71700033932814.049570681927e-060.0001293769080605
CTCF#1066435.360256373075030.0064925092527670.0278972753167832
CTCFL#140690213.16431623931620.007433367036996010.0306742036420572
E2F1#186934.907389214879320.008460985347239390.0324527837482219
E2F6#187635.017155731697390.00791769806886330.0321407209504825
GATA1#2623313.56030814380040.0004009615963782630.0038741815305902
HMGN3#932438.178547723350590.001827766942164210.0108534314119109
MAX#414936.452555509007120.003721913834265510.0186218721345624
MYC#460935.22228187160940.007020843755740150.0293946643016936
RFX5#5993312.04791082719510.0005717246050312580.00483954822701083
SIN3A#2594235.408884726815140.006318961977991520.0276024120632171
SMC3#9126210.02995522995520.0126656379767470.0457268585679439
STAT1#6772320.70658749719920.0001125992441046670.00154631853452298
TFAP2A#7020316.5186343730450.0002218033880766340.00247779698869778
TFAP2C#7022310.80922860986020.0007916746575753130.00614277188428738
ZNF263#1012738.221841637010680.001799043925565870.0109168757505185



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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