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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:26, 17 September 2013


Full id: C607_small_cervical_Keratinocyte_Sebocyte_maxillary_normal_skin



Phase1 CAGE Peaks

Hg19::chr5:134906500..134906526,+p@chr5:134906500..134906526
+
Hg19::chr5:134906654..134906662,-p@chr5:134906654..134906662
-
Hg19::chr5:134906663..134906677,-p@chr5:134906663..134906677
-
Hg19::chr5:134906674..134906690,+p@chr5:134906674..134906690
+
Hg19::chr5:134906681..134906686,-p@chr5:134906681..134906686
-
Hg19::chr5:134906796..134906805,-p@chr5:134906796..134906805
-
Hg19::chr5:134906837..134906859,-p@chr5:134906837..134906859
-
Hg19::chr5:134906921..134906955,-p@chr5:134906921..134906955
-
Hg19::chr5:134907052..134907077,-p@chr5:134907052..134907077
-
Hg19::chr5:134907261..134907265,-p@chr5:134907261..134907265
-
Hg19::chr5:134907414..134907422,-p@chr5:134907414..134907422
-
Hg19::chr5:134914194..134914201,-p@chr5:134914194..134914201
-
Hg19::chr5:134914219..134914230,-p@chr5:134914219..134914230
-
Hg19::chr5:134914630..134914641,-p2@CXCL14
Hg19::chr5:134914673..134914692,-p1@CXCL14


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>

Uber Anatomy
Ontology termp-valuen
adult organism2.17e-23114
cerebral cortex2.71e-1125
pallium2.71e-1125
regional part of cerebral cortex1.64e-1022
cerebral hemisphere2.79e-1032
telencephalon1.43e-0934
gyrus3.05e-096
neocortex3.17e-0920
skin gland7.35e-092
epidermis gland7.35e-092
gland of integumental system7.35e-092
sebaceous gland7.35e-092
skin sebaceous gland7.35e-092
sweat gland7.35e-092
sweat gland placode7.35e-092
sebaceous gland placode7.35e-092
regional part of telencephalon1.69e-0832
temporal lobe3.18e-086
middle temporal gyrus4.16e-082
brain grey matter6.57e-0834
gray matter6.57e-0834
pre-chordal neural plate1.14e-0761
regional part of forebrain1.27e-0741
forebrain1.27e-0741
anterior neural tube1.27e-0741
future forebrain1.27e-0741
small intestine1.75e-074
intestine5.66e-0717
organ system subdivision9.93e-07223


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)
MA0003.10.0289908
MA0004.10.256222
MA0006.10.842675
MA0007.11.94933
MA0009.10.669377
MA0014.10.0332175
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.889224
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.16.58784
MA0048.10.441458
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.11.41431
MA0056.10
MA0057.10.0196406
MA0058.10.182945
MA0059.11.02688
MA0060.10.0671843
MA0061.11.64561
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.0206064
MA0074.11.60579
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.536866
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.11669
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.930697
MA0101.12.00227
MA0103.10.131472
MA0105.10.623178
MA0106.10.983008
MA0107.10.650533
MA0108.21.28312
MA0109.10
MA0111.10.215855
MA0113.11.7945
MA0114.10.0920489
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.10.180729
MA0142.11.2271
MA0143.10.391385
MA0144.10.0838502
MA0145.10.135956
MA0146.10.00187713
MA0147.10.670164
MA0148.10.276339
MA0149.10.298252
MA0062.20.425026
MA0035.20.305721
MA0039.20.000100247
MA0138.20.425279
MA0002.20.220677
MA0137.20.153033
MA0104.20.236755
MA0047.20.366327
MA0112.20.00868143
MA0065.20.0103297
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.15.76274
MA0154.10.0723831
MA0155.10.0077078
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.10.000900738
MA0163.10.0031263
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.839067
MA0079.25.17282e-08
MA0102.21.1957
MA0258.10.0785319
MA0259.10.104286
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#1066482.858803398973350.002681647271099090.0147731068333325
ZNF274#107822189.5661538461545.12374436226736e-050.000872381378302642



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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