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{{Coexpression_clusters
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|full_id=C718_epididymis_seminal_uterus_cervix_ductus_peripheral_colon
|id=C718
}}

Latest revision as of 11:29, 17 September 2013


Full id: C718_epididymis_seminal_uterus_cervix_ductus_peripheral_colon



Phase1 CAGE Peaks

Hg19::chr10:119301969..119301989,-p3@EMX2OS
Hg19::chr10:119301997..119302022,-p5@EMX2OS
Hg19::chr10:119302025..119302049,-p4@EMX2OS
Hg19::chr10:119302051..119302077,-p8@EMX2OS
Hg19::chr10:119302093..119302108,-p6@EMX2OS
Hg19::chr10:119302150..119302163,+p8@EMX2
Hg19::chr10:119302182..119302196,+p6@EMX2
Hg19::chr10:119302232..119302265,+p1@EMX2
Hg19::chr10:119302268..119302282,+p4@EMX2
Hg19::chr10:119302508..119302559,+p5@EMX2
Hg19::chr10:119307702..119307723,+p10@EMX2


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
skin fibroblast1.55e-1123
Uber Anatomy
Ontology termp-valuen
regional part of forebrain7.42e-3841
forebrain7.42e-3841
anterior neural tube7.42e-3841
future forebrain7.42e-3841
regional part of nervous system1.01e-3653
regional part of brain1.01e-3653
neural tube2.57e-3556
neural rod2.57e-3556
future spinal cord2.57e-3556
neural keel2.57e-3556
telencephalon8.83e-3534
brain grey matter1.77e-3434
gray matter1.77e-3434
adult organism1.93e-34114
central nervous system5.03e-3481
cerebral hemisphere4.07e-3332
regional part of telencephalon9.04e-3332
nervous system5.85e-3289
brain3.27e-3168
future brain3.27e-3168
pre-chordal neural plate7.83e-3061
neural plate2.48e-2682
presumptive neural plate2.48e-2682
cerebral cortex4.00e-2625
pallium4.00e-2625
neurectoderm1.19e-2586
regional part of cerebral cortex2.40e-2322
ecto-epithelium3.66e-21104
neocortex5.22e-2120
ectoderm-derived structure8.65e-18171
ectoderm8.65e-18171
presumptive ectoderm8.65e-18171
structure with developmental contribution from neural crest7.50e-16132
basal ganglion2.93e-109
nuclear complex of neuraxis2.93e-109
aggregate regional part of brain2.93e-109
collection of basal ganglia2.93e-109
cerebral subcortex2.93e-109
integument3.56e-1046
integumental system3.56e-1046
neural nucleus1.03e-099
nucleus of brain1.03e-099
multi-cellular organism9.85e-09656
skin of body1.23e-0841
telencephalic nucleus4.48e-087
gyrus5.03e-086
organ part7.18e-08218
organ system subdivision1.56e-07223
organ3.18e-07503
limbic system3.86e-075
occipital lobe8.13e-075


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)
MA0003.10.486434
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.00227771
MA0017.10.682686
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.11.60736
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.11.96019
MA0052.10.716602
MA0055.10.0496191
MA0056.10
MA0057.11.53339
MA0058.10.265212
MA0059.10.2641
MA0060.13.16218
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.556338
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.13.85623e-06
MA0074.12.91489
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.0234479
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.10.405425
MA0141.12.05996
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.02761
MA0146.12.30635
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.000152622
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.21.14277
MA0065.20.0286783
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.10.462858
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.14.52806
MA0160.10.386031
MA0161.10
MA0162.10.178494
MA0163.10.232847
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.21.17095
MA0102.21.32663
MA0258.10.831523
MA0259.10.168926
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
CTBP2#14881057.01545485393471.13419318602184e-172.43232037279128e-15
EGR1#1958104.534708268009229.42307184802989e-074.03334508498522e-05
JUND#372795.722906861530841.04100398324849e-064.34364422718693e-05
NANOG#799231026.5861622554662.31327859661626e-143.88418815678466e-12
POLR2A#5430101.952230160507340.00304073181841430.0161318190787042
SP1#6667105.180346707400822.55812246304286e-071.32853183449892e-05
SUZ12#235121045.5598008282391.06787563003087e-162.14889909296327e-14
TCF12#693898.700925829061622.64468895283201e-081.82436373543476e-06
YY1#752894.018230613516792.20696821385449e-050.00048382357952718
ZNF263#10127107.474401488191526.91943485229632e-095.39700415637771e-07



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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