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Coexpression cluster:C1636: Difference between revisions

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Created page with "{{Coexpression_clusters |full_id=C1636_Mesenchymal_Alveolar_Placental_Smooth_Fibroblast_Bronchial_Hair |id=C1636 }}"
 
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{{Coexpression_clusters
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complex!0.0126567374393484!6050$GO:0004045!aminoacyl-tRNA hydrolase activity!0.0126567374393484!138428$GO:0008428!ribonuclease inhibitor activity!0.0126567374393484!6050$GO:0030128!clathrin coat of endocytic vesicle!0.0151827206402137!1175$GO:0030669!clathrin-coated endocytic vesicle membrane!0.0151827206402137!1175$GO:0030122!AP-2 adaptor complex!0.0151827206402137!1175$GO:0030666!endocytic vesicle membrane!0.0151827206402137!1175$GO:0045334!clathrin-coated endocytic vesicle!0.0151827206402137!1175$GO:0006901!vesicle coating!0.0151827206402137!1175$GO:0048268!clathrin cage assembly!0.0151827206402137!1175$GO:0006900!membrane budding!0.0155268682942639!1175$GO:0030132!clathrin coat of coated pit!0.0205538827115248!1175$GO:0016050!vesicle organization and biogenesis!0.023347032623047!1175$GO:0030125!clathrin vesicle coat!0.0272573686613283!1175$GO:0030139!endocytic vesicle!0.0272573686613283!1175$GO:0030665!clathrin coated vesicle membrane!0.0272573686613283!1175$GO:0006402!mRNA catabolic process!0.0323349158877492!6050$GO:0030100!regulation of endocytosis!0.0357932574808114!1175$GO:0045765!regulation of angiogenesis!0.037889819044312!6050$GO:0005905!coated pit!0.0407195667967789!1175$GO:0006401!RNA catabolic process!0.040882474854515!6050$GO:0030120!vesicle coat!0.040882474854515!1175$GO:0030662!coated vesicle membrane!0.040882474854515!1175$GO:0030131!clathrin adaptor complex!0.040882474854515!1175$GO:0030119!AP-type membrane coat adaptor complex!0.040882474854515!1175$GO:0030118!clathrin 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|full_id=C1636_Mesenchymal_Alveolar_Placental_Smooth_Fibroblast_Bronchial_Hair
|id=C1636
}}

Latest revision as of 11:49, 17 September 2013


Full id: C1636_Mesenchymal_Alveolar_Placental_Smooth_Fibroblast_Bronchial_Hair



Phase1 CAGE Peaks

Hg19::chr11:507184..507269,-p1@RNH1
Hg19::chr17:1945301..1945344,+p1@OVCA2
Hg19::chr19:47354082..47354132,-p1@AP2S1
Hg19::chr22:50963976..50964055,-p1@SCO2
Hg19::chr9:130477912..130477961,-p1@PTRH1


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:0032311angiogenin-PRI complex0.0126567374393484
GO:0004045aminoacyl-tRNA hydrolase activity0.0126567374393484
GO:0008428ribonuclease inhibitor activity0.0126567374393484
GO:0030128clathrin coat of endocytic vesicle0.0151827206402137
GO:0030669clathrin-coated endocytic vesicle membrane0.0151827206402137
GO:0030122AP-2 adaptor complex0.0151827206402137
GO:0030666endocytic vesicle membrane0.0151827206402137
GO:0045334clathrin-coated endocytic vesicle0.0151827206402137
GO:0006901vesicle coating0.0151827206402137
GO:0048268clathrin cage assembly0.0151827206402137
GO:0006900membrane budding0.0155268682942639
GO:0030132clathrin coat of coated pit0.0205538827115248
GO:0016050vesicle organization and biogenesis0.023347032623047
GO:0030125clathrin vesicle coat0.0272573686613283
GO:0030139endocytic vesicle0.0272573686613283
GO:0030665clathrin coated vesicle membrane0.0272573686613283
GO:0006402mRNA catabolic process0.0323349158877492
GO:0030100regulation of endocytosis0.0357932574808114
GO:0045765regulation of angiogenesis0.037889819044312
GO:0005905coated pit0.0407195667967789
GO:0006401RNA catabolic process0.040882474854515
GO:0030120vesicle coat0.040882474854515
GO:0030662coated vesicle membrane0.040882474854515
GO:0030131clathrin adaptor complex0.040882474854515
GO:0030119AP-type membrane coat adaptor complex0.040882474854515
GO:0030118clathrin coat0.0480117110439507



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
somatic cell9.77e-36588
animal cell3.16e-35679
eukaryotic cell3.16e-35679
mesodermal cell3.70e-29121
embryonic cell1.25e-28250
native cell1.26e-20722
contractile cell4.71e-1959
muscle precursor cell9.45e-1858
myoblast9.45e-1858
multi-potent skeletal muscle stem cell9.45e-1858
muscle cell6.55e-1755
smooth muscle cell6.88e-1543
smooth muscle myoblast6.88e-1543
electrically responsive cell8.21e-1561
electrically active cell8.21e-1561
non-terminally differentiated cell4.91e-13106
vascular associated smooth muscle cell1.78e-1232
epithelial cell2.74e-12253
meso-epithelial cell1.46e-1145
endothelial cell2.79e-1136
lining cell6.11e-1158
barrier cell6.11e-1158
fibroblast1.13e-0876
somatic stem cell3.53e-08433
multi fate stem cell7.49e-08427
blood vessel endothelial cell9.33e-0818
embryonic blood vessel endothelial progenitor cell9.33e-0818
epithelial cell of nephron1.68e-0715
endothelial cell of vascular tree2.16e-0724
stem cell5.24e-07441
Uber Anatomy
Ontology termp-valuen
epithelial vesicle4.40e-2278
multilaminar epithelium3.14e-1983
somite1.55e-1871
presomitic mesoderm1.55e-1871
presumptive segmental plate1.55e-1871
dermomyotome1.55e-1871
trunk paraxial mesoderm1.55e-1871
unilaminar epithelium2.94e-18148
vasculature3.17e-1878
vascular system3.17e-1878
dense mesenchyme tissue3.71e-1873
paraxial mesoderm5.02e-1872
presumptive paraxial mesoderm5.02e-1872
splanchnic layer of lateral plate mesoderm4.20e-1783
epithelial tube4.51e-17117
vessel1.55e-1668
epithelial tube open at both ends6.85e-1659
blood vessel6.85e-1659
blood vasculature6.85e-1659
vascular cord6.85e-1659
skeletal muscle tissue2.73e-1562
striated muscle tissue2.73e-1562
myotome2.73e-1562
artery4.51e-1542
arterial blood vessel4.51e-1542
arterial system4.51e-1542
mesoderm1.25e-14315
mesoderm-derived structure1.25e-14315
presumptive mesoderm1.25e-14315
mesenchyme2.71e-14160
entire embryonic mesenchyme2.71e-14160
trunk mesenchyme6.11e-14122
muscle tissue7.61e-1464
musculature7.61e-1464
musculature of body7.61e-1464
trunk7.78e-14199
organism subdivision9.42e-14264
circulatory system2.28e-13112
cardiovascular system4.40e-13109
systemic artery6.17e-1133
systemic arterial system6.17e-1133
lateral plate mesoderm2.52e-08203
blood vessel endothelium9.33e-0818
endothelium9.33e-0818
cardiovascular system endothelium9.33e-0818
musculoskeletal system1.28e-07167
nephron epithelium1.68e-0715
renal tubule1.68e-0715
nephron tubule1.68e-0715
nephron1.68e-0715
uriniferous tubule1.68e-0715
nephrogenic mesenchyme1.68e-0715
parenchyma2.05e-0715
multi-cellular organism3.04e-07656
simple squamous epithelium3.22e-0722
squamous epithelium4.07e-0725
anatomical system4.73e-07624
anatomical group5.08e-07625
cell layer5.53e-07309
epithelium8.40e-07306


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)
MA0003.11.04569
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.11.02528
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.11.29981
MA0059.10.522232
MA0060.10.860776
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.362215
MA0074.10.730989
MA0076.12.29573
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.946108
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.23.02043
MA0035.20.691506
MA0039.23.98195
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.12.24205
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.14.22787
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.53298
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
BRF2#552901214.915116279070.004644397888135530.0219254292383034
CHD2#110636.206413700470110.007774550126275590.0319457937851869
E2F1#186954.907389214879320.0003512818099256460.00352188931043722
EGR1#195843.990543275848110.0067800983001440.0287567692644874
ELF1#199743.406478367046030.01235066105299550.0447242013007106
ELK4#200539.741408995080820.00212558656574340.0122859115246929
ESR1#2099318.46116197769270.000326633459097560.00333007339268744
ETS1#211335.83725655332140.009253279045631430.0349652017166577
GABPB1#255345.654147068945740.001776696502096670.0109041785263251
IRF1#365957.63716375356393.84754333311872e-050.000723372777979454
MXI1#460135.976942977255580.008653004889366880.0329400830195221
MYC#460944.177825497287520.005691969036823440.0256687920133341
PBX3#5090313.14870761204650.0008860469322808430.00660135936370945
POU2F2#545235.463674434645510.01115650094469780.0410012598410616
SIN3A#2594244.327107781452110.004977052855762880.023237445715187
SIX5#147912310.25202921327540.001832291068677690.0108476076708593
SP1#666744.558705102512720.00407573565781680.0194759222349345
TAF1#687253.343046285745290.002394600090870310.0135154366023781
USF1#739156.361499277207969.59569864925045e-050.00136721032909832
YY1#752843.928936599883080.007193866269917620.0298320507986471
ZNF143#770238.100525931336740.003624870512090980.0183268553716546



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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