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{{Coexpression_clusters
{
|full_id=C363_Mallassezderived_Gingival_Keratinocyte_Mammary_Prostate_Small_Urothelial
 

Latest revision as of 11:21, 17 September 2013


Full id: C363_Mallassezderived_Gingival_Keratinocyte_Mammary_Prostate_Small_Urothelial



Phase1 CAGE Peaks

Hg19::chr18:21452899..21452910,+p2@LAMA3
Hg19::chr18:21452964..21452993,+p1@LAMA3
Hg19::chr18:21461943..21461955,+p@chr18:21461943..21461955
+
Hg19::chr18:21464760..21464772,+p2@X77598
Hg19::chr18:21474288..21474320,-p@chr18:21474288..21474320
-
Hg19::chr18:21474914..21474939,+p@chr18:21474914..21474939
+
Hg19::chr18:21474947..21474966,+p@chr18:21474947..21474966
+
Hg19::chr18:21478695..21478707,+p9@LAMA3
Hg19::chr18:21478968..21478985,-p@chr18:21478968..21478985
-
Hg19::chr18:21478996..21479008,-p@chr18:21478996..21479008
-
Hg19::chr18:21479321..21479334,+p@chr18:21479321..21479334
+
Hg19::chr18:21479368..21479399,-p@chr18:21479368..21479399
-
Hg19::chr18:21479408..21479415,-p@chr18:21479408..21479415
-
Hg19::chr18:21481109..21481120,+p@chr18:21481109..21481120
+
Hg19::chr18:21481125..21481150,+p@chr18:21481125..21481150
+
Hg19::chr18:21481209..21481225,+p@chr18:21481209..21481225
+
Hg19::chr18:21483933..21483967,-p@chr18:21483933..21483967
-
Hg19::chr18:21483996..21484010,+p@chr18:21483996..21484010
+
Hg19::chr18:21484533..21484572,+p@chr18:21484533..21484572
+
Hg19::chr18:21484604..21484624,+p@chr18:21484604..21484624
+
Hg19::chr18:21485515..21485536,-p@chr18:21485515..21485536
-
Hg19::chr18:21485558..21485596,-p@chr18:21485558..21485596
-
Hg19::chr18:21487576..21487588,-p@chr18:21487576..21487588
-
Hg19::chr18:21487788..21487807,+p@chr18:21487788..21487807
+
Hg19::chr18:21487848..21487862,-p@chr18:21487848..21487862
-
Hg19::chr18:21494675..21494689,+p@chr18:21494675..21494689
+
Hg19::chr18:21500893..21500904,+p@chr18:21500893..21500904
+
Hg19::chr18:21508639..21508652,+p@chr18:21508639..21508652
+
Hg19::chr18:21529811..21529823,+p@chr18:21529811..21529823
+
Hg19::chr18:21531667..21531694,+p@chr18:21531667..21531694
+
Hg19::chr3:129513704..129513729,-p12@TMCC1


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:0045995regulation of embryonic development0.00988889675790024
GO:0005606laminin-1 complex0.00988889675790024
GO:0043256laminin complex0.00988889675790024
GO:0005605basal lamina0.0182777618173525
GO:0030334regulation of cell migration0.0182777618173525
GO:0030155regulation of cell adhesion0.0182777618173525
GO:0051270regulation of cell motility0.0182777618173525
GO:0040012regulation of locomotion0.0182777618173525
GO:0040011locomotion0.0182777618173525
GO:0005604basement membrane0.0182777618173525
GO:0044420extracellular matrix part0.0277102104427011
GO:0008544epidermis development0.0277102104427011
GO:0007398ectoderm development0.0277102104427011
GO:0016477cell migration0.0363450637728375
GO:0009790embryonic development0.0363450637728375
GO:0050793regulation of developmental process0.0363450637728375
GO:0009888tissue development0.0441633001453489
GO:0051674localization of cell0.0495626658089424
GO:0006928cell motility0.0495626658089424



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>

Uber Anatomy
Ontology termp-valuen
extraembryonic membrane5.48e-2714
membranous layer5.48e-2714
chorion9.45e-237
extraembryonic structure1.02e-1424
endoderm-derived structure9.43e-14160
endoderm9.43e-14160
presumptive endoderm9.43e-14160
placenta2.14e-134
allantois2.14e-134
organ component layer4.99e-1266
gingival epithelium1.38e-113
acellular anatomical structure4.27e-113
egg chorion4.27e-113
female organism5.75e-0941
orifice7.13e-0936
jaw skeleton9.31e-094
splanchnocranium9.31e-094
urinary system structure1.01e-0847
mammary gland1.20e-084
mammary bud1.20e-084
mammary ridge1.20e-084
mammary placode1.20e-084
epithelial bud1.59e-0837
renal system1.76e-0848
amnion5.39e-087
mixed endoderm/mesoderm-derived structure1.89e-0729
mucosa2.41e-0720
epithelium of mucosa4.48e-078
primary subdivision of cranial skeletal system4.54e-075
somatic layer of lateral plate mesoderm5.42e-078
surface structure9.48e-0799
Disease
Ontology termp-valuen
squamous cell carcinoma4.05e-1014


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)
MA0003.18.33795e-06
MA0004.10.629016
MA0006.10.124841
MA0007.10.586462
MA0009.10.406485
MA0014.12.55326e-06
MA0017.10.662194
MA0019.10.172846
MA0024.10.322368
MA0025.15.65705
MA0027.11.94566
MA0028.10.0349277
MA0029.10.337465
MA0030.10.328486
MA0031.10.279263
MA0038.10.446179
MA0040.10.342075
MA0041.10.672034
MA0042.10.0842644
MA0043.11.84767
MA0046.10.397506
MA0048.10.222735
MA0050.10.0846723
MA0051.10.142882
MA0052.10.345132
MA0055.10.131184
MA0056.10
MA0057.10.0199099
MA0058.11.59805
MA0059.10.735953
MA0060.10.00790927
MA0061.10.0861879
MA0063.10
MA0066.10.876715
MA0067.10.685278
MA0068.10.0514652
MA0069.10.394339
MA0070.10.385179
MA0071.10.780219
MA0072.10.381514
MA0073.11.62331e-11
MA0074.11.39176
MA0076.10.0564857
MA0077.12.61585
MA0078.10.205266
MA0081.10.418953
MA0083.10.412707
MA0084.10.860109
MA0087.10.379524
MA0088.10.0379179
MA0089.10
MA0090.10.484662
MA0091.10.306639
MA0092.10.258792
MA0093.10.878362
MA0095.10
MA0098.10
MA0100.10.153602
MA0101.10.130624
MA0103.10.519443
MA0105.10.0036969
MA0106.10.979904
MA0107.10.363169
MA0108.20.276987
MA0109.10
MA0111.10.513809
MA0113.10.180801
MA0114.10.177592
MA0115.10.615724
MA0116.10.190388
MA0117.10.437859
MA0119.10.386297
MA0122.10.459779
MA0124.10.578498
MA0125.11.2591
MA0130.10
MA0131.10.621676
MA0132.10
MA0133.10
MA0135.10.431776
MA0136.10.149526
MA0139.10.164946
MA0140.10.773759
MA0141.11.12234
MA0142.10.255934
MA0143.10.180914
MA0144.10.157126
MA0145.10.0001685
MA0146.10.00211819
MA0147.10.380954
MA0148.10.102785
MA0149.10.116654
MA0062.20.00468224
MA0035.20.772048
MA0039.26.401e-05
MA0138.20.20609
MA0002.20.103088
MA0137.20.145957
MA0104.20.242912
MA0047.20.162866
MA0112.20.0427249
MA0065.20.0529546
MA0150.11.24113
MA0151.10
MA0152.10.78974
MA0153.10.489927
MA0154.10.0870334
MA0155.10.000960937
MA0156.10.0375332
MA0157.10.236372
MA0158.10
MA0159.10.942055
MA0160.10.723014
MA0161.10
MA0162.10.000117712
MA0163.12.17595e-07
MA0164.10.553088
MA0080.20.0312659
MA0018.20.171273
MA0099.20.790611
MA0079.21.17407e-13
MA0102.20.895427
MA0258.10.0528215
MA0259.10.40277
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

No analysis results for this cluster

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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