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{{Coexpression_clusters
{
|full_id=C511_Placental_Alveolar_Bronchial_amniotic_Gingival_Corneal_Mammary
 

Latest revision as of 11:24, 17 September 2013


Full id: C511_Placental_Alveolar_Bronchial_amniotic_Gingival_Corneal_Mammary



Phase1 CAGE Peaks

Hg19::chr11:394157..394180,+p3@PKP3
Hg19::chr11:394196..394258,+p1@PKP3
Hg19::chr11:394263..394275,+p5@PKP3
Hg19::chr11:66824276..66824298,+p2@RHOD
Hg19::chr11:66824303..66824343,+p1@RHOD
Hg19::chr11:66824346..66824359,+p3@RHOD
Hg19::chr14:105330834..105330858,+p@chr14:105330834..105330858
+
Hg19::chr17:7284402..7284414,+p1@TNK1
Hg19::chr19:45843994..45844015,+p1@KLC3
Hg19::chr1:35246775..35246797,+p2@GJB3
Hg19::chr1:35246802..35246823,+p1@GJB3
Hg19::chr1:35247135..35247151,+p9@GJB3
Hg19::chr1:35247162..35247173,+p7@GJB3
Hg19::chr1:35247859..35247901,+p5@GJB3
Hg19::chr5:175843524..175843547,-p1@CLTB
Hg19::chr6:41604725..41604741,+p4@MDFI
Hg19::chr6:41604747..41604796,+p1@MDFI
Hg19::chr9:140506925..140506963,+p3@ARRDC1


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:0014704intercalated disc0.00971357311575209
GO:0005911intercellular junction0.0328503730566494
GO:0009950dorsal/ventral axis specification0.0328503730566494
GO:0005243gap junction channel activity0.0328503730566494
GO:0022829wide pore channel activity0.0328503730566494
GO:0043392negative regulation of DNA binding0.0328503730566494
GO:0051100negative regulation of binding0.0328503730566494
GO:0042994cytoplasmic sequestering of transcription factor0.0328503730566494
GO:0030057desmosome0.0328503730566494
GO:0051220cytoplasmic sequestering of protein0.0328503730566494
GO:0042308negative regulation of protein import into nucleus0.0328503730566494
GO:0042992negative regulation of transcription factor import into nucleus0.0328503730566494
GO:0051101regulation of DNA binding0.0328503730566494
GO:0046823negative regulation of nucleocytoplasmic transport0.0328503730566494
GO:0051224negative regulation of protein transport0.0328503730566494
GO:0030132clathrin coat of coated pit0.0328503730566494
GO:0001890placenta development0.0328503730566494
GO:0030054cell junction0.0328503730566494
GO:0030130clathrin coat of trans-Golgi network vesicle0.0328503730566494
GO:0012510trans-Golgi network transport vesicle membrane0.0328503730566494
GO:0009798axis specification0.0328503730566494
GO:0030178negative regulation of Wnt receptor signaling pathway0.0328503730566494
GO:0005886plasma membrane0.0328503730566494
GO:0007257activation of JNK activity0.0328503730566494
GO:0042990regulation of transcription factor import into nucleus0.0328503730566494
GO:0042991transcription factor import into nucleus0.0328503730566494
GO:0030125clathrin vesicle coat0.0328503730566494
GO:0042306regulation of protein import into nucleus0.0328503730566494
GO:0033157regulation of intracellular protein transport0.0328503730566494
GO:0043507positive regulation of JNK activity0.0328503730566494
GO:0030665clathrin coated vesicle membrane0.0328503730566494
GO:0006886intracellular protein transport0.0328503730566494
GO:0032507maintenance of cellular protein localization0.0328503730566494
GO:0043506regulation of JNK activity0.0328503730566494
GO:0051651maintenance of cellular localization0.0328503730566494
GO:0032386regulation of intracellular transport0.0328503730566494
GO:0045185maintenance of protein localization0.0328503730566494
GO:0030111regulation of Wnt receptor signaling pathway0.0328503730566494
GO:0051223regulation of protein transport0.0328503730566494
GO:0009953dorsal/ventral pattern formation0.0328503730566494
GO:0005922connexon complex0.0328503730566494
GO:0051098regulation of binding0.0328503730566494
GO:0005871kinesin complex0.0328503730566494
GO:0046822regulation of nucleocytoplasmic transport0.0328503730566494
GO:0030140trans-Golgi network transport vesicle0.0328503730566494
GO:0051051negative regulation of transport0.0336156853620909
GO:0030658transport vesicle membrane0.0336156853620909
GO:0030660Golgi-associated vesicle membrane0.0339741446877352
GO:0005921gap junction0.0353546012067987
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0407401896373074
GO:0051235maintenance of localization0.040936282410428
GO:0044459plasma membrane part0.0413010282697245
GO:0005905coated pit0.0413057609230136
GO:0046777protein amino acid autophosphorylation0.0414799877126929
GO:0016540protein autoprocessing0.0425694626794528
GO:0030120vesicle coat0.0454288408777507
GO:0030662coated vesicle membrane0.0455204621896562
GO:0000187activation of MAPK activity0.049972168624338



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
endoderm-derived structure1.42e-28160
endoderm1.42e-28160
presumptive endoderm1.42e-28160
digestive system4.89e-20145
digestive tract4.89e-20145
primitive gut4.89e-20145
respiratory system1.27e-1974
subdivision of digestive tract2.74e-16118
respiratory tract2.59e-1554
urinary system structure2.12e-1447
renal system6.96e-1448
foregut8.92e-1387
respiratory primordium1.41e-1238
endoderm of foregut1.41e-1238
orifice5.70e-1236
segment of respiratory tract7.17e-1247
extraembryonic membrane1.11e-1114
membranous layer1.11e-1114
endo-epithelium8.31e-1082
epithelial bud9.96e-1037
oral opening2.71e-0922
anatomical space4.32e-0995
chorion6.93e-097
organ part9.42e-09218
nephron tubule epithelium1.45e-0810
epithelial fold3.92e-0847
larynx5.63e-089
trunk region element6.07e-08101
organ6.64e-08503
upper respiratory tract1.72e-0719
thoracic cavity element2.09e-0734
thoracic cavity2.09e-0734
organism subdivision2.13e-07264
reproductive structure3.14e-0759
reproductive system3.14e-0759
thoracic segment organ4.90e-0735
transitional epithelium5.15e-076
mouth5.51e-0729
stomodeum5.51e-0729
mucosa6.98e-0720
excretory tube7.90e-0716
kidney epithelium7.90e-0716
immaterial anatomical entity8.34e-07117
urothelium8.70e-075
Disease
Ontology termp-valuen
carcinoma1.04e-25106
cell type cancer1.34e-15143
squamous cell carcinoma8.20e-1414
adenocarcinoma1.40e-1125


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)
MA0003.15.19209
MA0004.10.207008
MA0006.10.101986
MA0007.10.564363
MA0009.10.600198
MA0014.11.81849
MA0017.10.395274
MA0019.10.322194
MA0024.11.25925
MA0025.10.725013
MA0027.12.18072
MA0028.11.19395
MA0029.10.522011
MA0030.10.511665
MA0031.10.454061
MA0038.10.285594
MA0040.10.527306
MA0041.10.220669
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.11.89858
MA0050.10.197941
MA0051.10.282227
MA0052.10.530811
MA0055.10.0623184
MA0056.10
MA0057.10.493527
MA0058.10.141262
MA0059.10.140431
MA0060.10.0444001
MA0061.10.137405
MA0063.10
MA0066.10.779889
MA0067.10.900956
MA0068.10.0222576
MA0069.10.586593
MA0070.10.576293
MA0071.10.255111
MA0072.10.572162
MA0073.10.272787
MA0074.10.281628
MA0076.10.461922
MA0077.10.565087
MA0078.10.363755
MA0081.10.434032
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.11.58883
MA0089.10
MA0090.12.15471
MA0091.10.208918
MA0092.10.181853
MA0093.10.103729
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.10.105632
MA0103.11.61454
MA0105.11.30924
MA0106.10.854542
MA0107.10.0664936
MA0108.20.451357
MA0109.10
MA0111.10.508569
MA0113.11.58989
MA0114.10.852422
MA0115.10.827474
MA0116.11.84948
MA0117.10.635078
MA0119.10.810503
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.791942
MA0139.10.860218
MA0140.10.253051
MA0141.10.849848
MA0142.10.426146
MA0143.10.332682
MA0144.11.21536
MA0145.14.624
MA0146.17.43838
MA0147.10.245602
MA0148.10.225411
MA0149.10.245595
MA0062.22.24104
MA0035.20.252505
MA0039.25.60909
MA0138.20.364793
MA0002.20.155585
MA0137.20.368913
MA0104.20.168935
MA0047.20.309071
MA0112.25.02962
MA0065.20.526971
MA0150.10.476082
MA0151.10
MA0152.10.258148
MA0153.10.692238
MA0154.13.02862
MA0155.10.273665
MA0156.10.749879
MA0157.10.402372
MA0158.10
MA0159.10.0701863
MA0160.11.24066
MA0161.10
MA0162.11.70269
MA0163.14.15577
MA0164.10.342871
MA0080.21.67871
MA0018.20.320136
MA0099.20.716923
MA0079.23.59357
MA0102.21.11935
MA0258.11.63799
MA0259.10.547239
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
E2F1#186992.453694607439660.004849080951923650.0227252934950843
GABPB1#255383.141192816080970.001854476277993430.0109435895579928
NR3C1#290864.991007777057680.0008156830055758030.0062150082016
POLR2A#5430182.147453176558071.059158074972e-064.41410256153236e-05
SMARCC1#659937.277226553271910.007571580574644320.0312075576634942



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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