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{{Coexpression_clusters
{
|full_id=C359_xeroderma_tonsil_acute_colon_lymph_trachea_bladder
 

Latest revision as of 11:21, 17 September 2013


Full id: C359_xeroderma_tonsil_acute_colon_lymph_trachea_bladder



Phase1 CAGE Peaks

Hg19::chr11:131056606..131056628,-p@chr11:131056606..131056628
-
Hg19::chr11:32154200..32154208,+p1@ENST00000525133
Hg19::chr11:33676379..33676397,+p@chr11:33676379..33676397
+
Hg19::chr11:57182176..57182224,-p@chr11:57182176..57182224
-
Hg19::chr11:77150035..77150044,-p@chr11:77150035..77150044
-
Hg19::chr14:106329430..106329463,-p1@uc001yrw.1
p1@uc001ysj.2
p1@uc001ysk.1
p1@uc001ysl.1
Hg19::chr14:107170409..107170434,-p1@IGHV1-69
Hg19::chr14:75802600..75802617,+p@chr14:75802600..75802617
+
Hg19::chr14:75802635..75802649,+p@chr14:75802635..75802649
+
Hg19::chr15:55611565..55611576,+p7@PIGB
Hg19::chr17:76130076..76130100,-p@chr17:76130076..76130100
-
Hg19::chr17:9955844..9955857,-p@chr17:9955844..9955857
-
Hg19::chr17:9955874..9955881,-p@chr17:9955874..9955881
-
Hg19::chr18:56203145..56203154,+p@chr18:56203145..56203154
+
Hg19::chr18:67613122..67613129,-p@chr18:67613122..67613129
-
Hg19::chr19:7766976..7766982,-p9@FCER2
Hg19::chr1:101837029..101837058,+p@chr1:101837029..101837058
+
Hg19::chr1:101914223..101914228,-p@chr1:101914223..101914228
-
Hg19::chr1:111682499..111682513,+p5@CEPT1
Hg19::chr1:111772329..111772341,+p7@CHI3L2
Hg19::chr1:111772350..111772370,+p3@CHI3L2
Hg19::chr1:111772381..111772415,+p2@CHI3L2
Hg19::chr1:111772435..111772463,+p4@CHI3L2
Hg19::chr1:152880744..152880747,+p3@IVL
Hg19::chr1:152880760..152880771,+p2@IVL
Hg19::chr22:23055620..23055631,+p1@DQ234400
Hg19::chr22:23055632..23055638,+p3@DQ234400
Hg19::chr22:26346329..26346352,+p@chr22:26346329..26346352
+
Hg19::chr4:5364767..5364769,+p@chr4:5364767..5364769
+
Hg19::chr7:55583740..55583751,-p5@VOPP1
Hg19::chr7:70241758..70241770,+p47@AUTS2


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:0008654phospholipid biosynthetic process0.010737464781943
GO:0046467membrane lipid biosynthetic process0.010737464781943
GO:0018153isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine0.010737464781943
GO:0018262isopeptide cross-linking0.010737464781943
GO:0018199peptidyl-glutamine modification0.010737464781943
GO:0004307ethanolaminephosphotransferase activity0.0111736804937354
GO:0004142diacylglycerol cholinephosphotransferase activity0.0111736804937354
GO:0006644phospholipid metabolic process0.0111736804937354
GO:0019863IgE binding0.0142568348656904
GO:0006643membrane lipid metabolic process0.0142568348656904
GO:0010224response to UV-B0.0146376878124516
GO:0008610lipid biosynthetic process0.0165118839613148
GO:0017169CDP-alcohol phosphatidyltransferase activity0.0165118839613148
GO:0018205peptidyl-lysine modification0.0172477522886803
GO:0006032chitin catabolic process0.0186546222107435
GO:0006046N-acetylglucosamine catabolic process0.0186546222107435
GO:0005789endoplasmic reticulum membrane0.0186546222107435
GO:0006043glucosamine catabolic process0.0186546222107435
GO:0046348amino sugar catabolic process0.0186546222107435
GO:0006030chitin metabolic process0.0186546222107435
GO:0004568chitinase activity0.0186546222107435
GO:0042175nuclear envelope-endoplasmic reticulum network0.0186546222107435
GO:0019865immunoglobulin binding0.0186546222107435
GO:0044432endoplasmic reticulum part0.0208492312452853
GO:0044247cellular polysaccharide catabolic process0.0208492312452853
GO:0000272polysaccharide catabolic process0.0208492312452853
GO:0016780phosphotransferase activity, for other substituted phosphate groups0.0208492312452853
GO:0001533cornified envelope0.0210604286585
GO:0018149peptide cross-linking0.0240242630131579
GO:0000030mannosyltransferase activity0.0241148894453259
GO:0006506GPI anchor biosynthetic process0.0250619670405395
GO:0030216keratinocyte differentiation0.0251141318157448
GO:0006505GPI anchor metabolic process0.0251630157626931
GO:0009411response to UV0.0253310637807865
GO:0006044N-acetylglucosamine metabolic process0.0253310637807865
GO:0046489phosphoinositide biosynthetic process0.0253310637807865
GO:0006041glucosamine metabolic process0.0253310637807865
GO:0031424keratinization0.0267667332897792
GO:0044255cellular lipid metabolic process0.0267667332897792
GO:0006040amino sugar metabolic process0.0267667332897792
GO:0005178integrin binding0.0267667332897792
GO:0046474glycerophospholipid biosynthetic process0.0293051626849468
GO:0009913epidermal cell differentiation0.0304836773360426
GO:0006497protein amino acid lipidation0.0319707530670764
GO:0042158lipoprotein biosynthetic process0.0319707530670764
GO:0048730epidermis morphogenesis0.0319707530670764
GO:0005783endoplasmic reticulum0.0320917655350622
GO:0006629lipid metabolic process0.0341520913372628
GO:0048729tissue morphogenesis0.0384680295948203
GO:0012505endomembrane system0.0384680295948203
GO:0030384phosphoinositide metabolic process0.0415056245270081
GO:0009416response to light stimulus0.0415056245270081
GO:0042157lipoprotein metabolic process0.0415056245270081
GO:0044264cellular polysaccharide metabolic process0.0415056245270081
GO:0005976polysaccharide metabolic process0.0417151002173427
GO:0030674protein binding, bridging0.0433362327013298
GO:0006650glycerophospholipid metabolic process0.0456192018890636
GO:0009314response to radiation0.0456192018890636
GO:0032403protein complex binding0.0456192018890636



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
hemopoietic organ1.38e-497
immune organ1.38e-497
spleen1.65e-423
gastrointestinal system mesentery1.65e-423
stomach region1.65e-423
mesentery1.65e-423
gastrointestinal system serosa1.65e-423
mesentery of stomach1.65e-423
gut mesentery1.65e-423
dorsal mesentery1.65e-423
dorsal mesogastrium1.65e-423
peritoneal cavity1.65e-423
spleen primordium1.65e-423
stomach2.04e-168
food storage organ2.04e-168
tonsil2.06e-151
mucosa-associated lymphoid tissue2.06e-151
lymphoid tissue2.06e-151
tonsillar ring2.06e-151
thymus7.47e-154
hemolymphoid system gland7.47e-154
thymic region7.47e-154
pharyngeal gland7.47e-154
thymus primordium7.47e-154
chordate pharynx3.58e-1310
pharyngeal region of foregut3.58e-1310
mixed endoderm/mesoderm-derived structure4.63e-1229
pharynx4.96e-1211
cavity lining3.73e-1112
serous membrane3.73e-1112
intraembryonic coelom3.73e-1112
pharyngeal epithelium3.19e-106
viscus1.28e-0718
upper respiratory tract3.36e-0719
Disease
Ontology termp-valuen
genetic disease5.56e-161
monogenic disease5.56e-161
xeroderma pigmentosum5.56e-161


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
MA0004.11.05161
MA0006.10.296883
MA0007.10.0818413
MA0009.10.406485
MA0014.10.000431182
MA0017.10.0420572
MA0019.10.514288
MA0024.10.322368
MA0025.10.520106
MA0027.11.94566
MA0028.10.0349277
MA0029.10.337465
MA0030.10.328486
MA0031.10.279263
MA0038.10.875651
MA0040.10.342075
MA0041.11.64074
MA0042.12.05617
MA0043.10.406746
MA0046.10.397506
MA0048.10.357342
MA0050.11.00941
MA0051.10.439954
MA0052.10.345132
MA0055.11.8661
MA0056.10
MA0057.10.0533884
MA0058.11.59805
MA0059.11.59096
MA0060.10.00790927
MA0061.11.42356
MA0063.10
MA0066.10.446809
MA0067.10.685278
MA0068.10.231182
MA0069.10.394339
MA0070.10.385179
MA0071.10.780219
MA0072.10.381514
MA0073.10.000812926
MA0074.10.142444
MA0076.10.206609
MA0077.10.37525
MA0078.10.205266
MA0081.10.418953
MA0083.10.412707
MA0084.10.860109
MA0087.10.379524
MA0088.10.230385
MA0089.10
MA0090.10.836434
MA0091.10.0917987
MA0092.10.933982
MA0093.11.71165
MA0095.10
MA0098.10
MA0100.10.153602
MA0101.10.89179
MA0103.10.28031
MA0105.10.604146
MA0106.11.55826
MA0107.11.66189
MA0108.20.276987
MA0109.10
MA0111.10.513809
MA0113.10.180801
MA0114.10.0677467
MA0115.10.615724
MA0116.10.190388
MA0117.10.437859
MA0119.11.06133
MA0122.10.459779
MA0124.10.578498
MA0125.10.50452
MA0130.10
MA0131.10.217579
MA0132.10
MA0133.10
MA0135.10.431776
MA0136.10.149526
MA0139.10.0239134
MA0140.10.386354
MA0141.10.185774
MA0142.10.711177
MA0143.10.180914
MA0144.10.315342
MA0145.10.0995828
MA0146.10.0223147
MA0147.10.380954
MA0148.10.102785
MA0149.10.116654
MA0062.20.080735
MA0035.20.121502
MA0039.21.8879e-05
MA0138.20.594441
MA0002.21.19795
MA0137.20.145957
MA0104.20.42453
MA0047.20.162866
MA0112.20.0870721
MA0065.20.0223142
MA0150.12.28547
MA0151.10
MA0152.10.395672
MA0153.10.489927
MA0154.10.586815
MA0155.10.34085
MA0156.10.0375332
MA0157.10.236372
MA0158.10
MA0159.10.632503
MA0160.10.723014
MA0161.10
MA0162.10.027259
MA0163.10.00454359
MA0164.10.188828
MA0080.20.127678
MA0018.20.171273
MA0099.21.28721
MA0079.23.78023e-10
MA0102.20.895427
MA0258.10.144068
MA0259.10.208795
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
BCL11A#5333576.406005991137088.40163614903359e-050.00126125985017812
BCL3#60244.457690684353330.0118271718455860.0430854930545591
EBF1#1879154.309580732210812.89067900838075e-071.46340099348656e-05
IRF4#366253.53459882044260.01245197612670210.0450723299031865
NFKB1#4790162.832548864100042.68068349868494e-050.000574293136244423
POU2F2#545292.64371343611880.004891568891958950.0228884661069579
TCF12#693882.744378039273910.006663992092590880.0283552931414992
ZEB1#693563.268728777589130.008791263817974920.0333921589280435



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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