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{{Coexpression_clusters
{
|full_id=C249_nonsmall_small_smallcell_occipital_somatostatinoma_maxillary_medial
|gostat_on_coexpression_clusters

Latest revision as of 11:05, 17 September 2013


Full id: C249_nonsmall_small_smallcell_occipital_somatostatinoma_maxillary_medial



Phase1 CAGE Peaks

Hg19::chr10:5057199..5057247,-p@chr10:5057199..5057247
-
Hg19::chr10:5138199..5138209,+p@chr10:5138199..5138209
+
Hg19::chr11:13809056..13809057,+p@chr11:13809056..13809057
+
Hg19::chr11:69518108..69518118,-p@chr11:69518108..69518118
-
Hg19::chr11:69518332..69518343,-p@chr11:69518332..69518343
-
Hg19::chr11:69518781..69518797,-p1@FGF19
Hg19::chr11:69518856..69518859,-p2@FGF19
Hg19::chr12:57638896..57638928,-p@chr12:57638896..57638928
-
Hg19::chr12:79439461..79439490,+p2@SYT1
Hg19::chr16:2094808..2094822,-p@chr16:2094808..2094822
-
Hg19::chr17:46622205..46622218,-p3@HOXB2
Hg19::chr17:46667774..46667790,+p1@ENST00000476204
Hg19::chr17:46670845..46670856,-p8@AB464575
Hg19::chr17:46670894..46670923,-p3@AB464575
Hg19::chr17:46670939..46670958,-p5@AB464575
Hg19::chr17:46670967..46671005,-p2@AB464575
Hg19::chr17:46691990..46692004,-p11@HOXB8
Hg19::chr17:63096940..63096949,+p@chr17:63096940..63096949
+
Hg19::chr18:40857413..40857422,-p10@SYT4
Hg19::chr18:63412128..63412151,+p@chr18:63412128..63412151
+
Hg19::chr18:63412228..63412270,+p@chr18:63412228..63412270
+
Hg19::chr18:63418785..63418796,+p@chr18:63418785..63418796
+
Hg19::chr18:70210391..70210400,-p@chr18:70210391..70210400
-
Hg19::chr18:70210764..70210794,-p1@CBLN2
Hg19::chr18:70210848..70210853,-p9@CBLN2
Hg19::chr18:70211559..70211587,-p2@CBLN2
Hg19::chr19:42212501..42212521,+p2@CEACAM5
Hg19::chr19:51379271..51379283,+p3@KLK2
Hg19::chr19:51412411..51412426,-p4@KLK4
Hg19::chr19:51412626..51412645,-p1@KLK4
Hg19::chr19:51412658..51412666,-p3@KLK4
Hg19::chr1:179712011..179712021,+p5@FAM163A
Hg19::chr1:179712410..179712437,+p1@FAM163A
Hg19::chr1:179759377..179759381,+p@chr1:179759377..179759381
+
Hg19::chr1:246382944..246382951,-p@chr1:246382944..246382951
-
Hg19::chr1:246382967..246382990,-p@chr1:246382967..246382990
-
Hg19::chr1:246382992..246383003,-p@chr1:246382992..246383003
-
Hg19::chr22:29874053..29874064,-p2@ENST00000419368
Hg19::chr2:115918789..115918795,-p3@ENST00000448663
Hg19::chr2:115919597..115919632,-p@chr2:115919597..115919632
-
Hg19::chr2:115919726..115919782,+p1@DPP10
Hg19::chr2:149017229..149017235,-p@chr2:149017229..149017235
-
Hg19::chr2:32264588..32264595,-p@chr2:32264588..32264595
-
Hg19::chr4:116034979..116035046,-p1@NDST4
Hg19::chr4:116434644..116434654,+p@chr4:116434644..116434654
+
Hg19::chr4:158745392..158745410,-p@chr4:158745392..158745410
-
Hg19::chr4:93512357..93512364,+p@chr4:93512357..93512364
+
Hg19::chr5:95768762..95768786,-p4@PCSK1
Hg19::chr7:1968190..1968198,-p@chr7:1968190..1968198
-
Hg19::chr7:82136933..82136940,-p@chr7:82136933..82136940
-
Hg19::chr8:114058689..114058694,-p@chr8:114058689..114058694
-
Hg19::chr8:114449612..114449615,-p10@CSMD3
Hg19::chr8:13988549..13988555,+p@chr8:13988549..13988555
+


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

p.valueFDRnGenesnPathwayName
5.13066354040941e-050.0324771002107916222{MEIS1,22} (Static Module):NA



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:0008236serine-type peptidase activity0.000803614561659265
GO:0017171serine hydrolase activity0.000803614561659265
GO:0007269neurotransmitter secretion0.00568189744291423
GO:0045055regulated secretory pathway0.00701813690671022
GO:0004252serine-type endopeptidase activity0.00701813690671022
GO:0003001generation of a signal involved in cell-cell signaling0.00701813690671022
GO:0008021synaptic vesicle0.00701813690671022
GO:0004285proprotein convertase 1 activity0.00701813690671022
GO:0001505regulation of neurotransmitter levels0.00701813690671022
GO:0043005neuron projection0.00701813690671022
GO:0031410cytoplasmic vesicle0.00721540071865314
GO:0031982vesicle0.00721540071865314
GO:0017075syntaxin-1 binding0.00959444311424536
GO:0030136clathrin-coated vesicle0.0100678107420916
GO:0008233peptidase activity0.0104414470156899
GO:0016808proprotein convertase activity0.0109916190620399
GO:0030672synaptic vesicle membrane0.0109916190620399
GO:0006508proteolysis0.0109916190620399
GO:0030135coated vesicle0.0120608659594642
GO:0015016[heparan sulfate]-glucosamine N-sulfotransferase activity0.012468370782814
GO:0007267cell-cell signaling0.0128309169115166
GO:0004293tissue kallikrein activity0.0141661009808818
GO:0005513detection of calcium ion0.0205509979981514
GO:0050750low-density lipoprotein receptor binding0.0205509979981514
GO:0004175endopeptidase activity0.0205509979981514
GO:0045045secretory pathway0.0230651229498711
GO:0001755neural crest cell migration0.0230651229498711
GO:0035091phosphoinositide binding0.0233978588233504
GO:0004274dipeptidyl-peptidase IV activity0.0249015374584975
GO:0042734presynaptic membrane0.0249015374584975
GO:0007268synaptic transmission0.0262524939073007
GO:0014032neural crest cell development0.0262524939073007
GO:0014033neural crest cell differentiation0.0262524939073007
GO:0032940secretion by cell0.0262524939073007
GO:0017157regulation of exocytosis0.0262524939073007
GO:0042995cell projection0.0262524939073007
GO:0016021integral to membrane0.0262524939073007
GO:0031224intrinsic to membrane0.0262524939073007
GO:0019226transmission of nerve impulse0.0262524939073007
GO:0009593detection of chemical stimulus0.0262524939073007
GO:0005543phospholipid binding0.0262524939073007
GO:0019905syntaxin binding0.0262524939073007
GO:0005545phosphatidylinositol binding0.0262524939073007
GO:0008239dipeptidyl-peptidase activity0.0262524939073007
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.0262524939073007
GO:0016023cytoplasmic membrane-bound vesicle0.0266919997499756
GO:0031988membrane-bound vesicle0.026854517623632
GO:0000149SNARE binding0.0271928184573991
GO:0048762mesenchymal cell differentiation0.0292570676362738
GO:0014031mesenchymal cell development0.0292570676362738
GO:0046903secretion0.0292570676362738
GO:0032501multicellular organismal process0.03332856012265
GO:0030054cell junction0.034808570985521
GO:0016787hydrolase activity0.0362148258733129
GO:0004289subtilase activity0.0394556012910521
GO:0030141secretory granule0.040950932151947
GO:0044425membrane part0.0413705416999085
GO:0051260protein homooligomerization0.0437823996691124
GO:0005509calcium ion binding0.0451228328736624



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>

Cell Type
Ontology termp-valuen
lung fibroblast1.23e-661
epithelial cell of lung4.91e-1519
Disease
Ontology termp-valuen
lung cancer1.04e-1815
lung small cell carcinoma8.69e-184
respiratory system cancer1.27e-1716
bronchus cancer8.99e-117
bronchogenic carcinoma8.99e-117
lung carcinoma1.12e-089


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)
MA0003.10.225499
MA0004.11.5727
MA0006.10.170614
MA0007.10.236967
MA0009.10.6783
MA0014.10.700159
MA0017.10.92631
MA0019.10.899624
MA0024.10.518847
MA0025.10.338104
MA0027.11.7145
MA0028.10.0903589
MA0029.10.547244
MA0030.10.179432
MA0031.10.438433
MA0038.10.767512
MA0040.10.19001
MA0041.11.24004
MA0042.10.461809
MA0043.10.241959
MA0046.10.234388
MA0048.10.293155
MA0050.10.0231285
MA0051.10.194436
MA0052.10.192408
MA0055.10.333894
MA0056.10
MA0057.11.24693
MA0058.11.81421
MA0059.10.280702
MA0060.10.275863
MA0061.10.310177
MA0063.10
MA0066.10.199067
MA0067.10.486134
MA0068.12.03141
MA0069.10.231803
MA0070.10.224361
MA0071.10.161667
MA0072.10.630677
MA0073.15.87072
MA0074.10.429982
MA0076.10.0120651
MA0077.10.216348
MA0078.10.0906355
MA0081.10.137403
MA0083.12.76831
MA0084.10.649313
MA0087.10.21979
MA0088.10.254996
MA0089.10
MA0090.10.1745
MA0091.10.268617
MA0092.10.410987
MA0093.12.57256
MA0095.10
MA0098.10
MA0100.10.212741
MA0101.10.0820002
MA0103.11.6299
MA0105.10.412501
MA0106.10.0685575
MA0107.10.45184
MA0108.20.855409
MA0109.10
MA0111.10.374371
MA0113.10.551924
MA0114.10.432348
MA0115.11.08351
MA0116.11.19601
MA0117.10.267775
MA0119.10.120052
MA0122.10.780586
MA0124.10.38955
MA0125.10.324569
MA0130.10
MA0131.10.0988145
MA0132.10
MA0133.10
MA0135.10.26269
MA0136.10.056199
MA0139.10.265625
MA0140.10.0410132
MA0141.10.0490247
MA0142.10.125391
MA0143.10.260247
MA0144.10.238365
MA0145.11.47493
MA0146.10.177068
MA0147.10.479065
MA0148.10.556623
MA0149.10.0383072
MA0062.20.0222718
MA0035.20.0408122
MA0039.21.69196
MA0138.20.304949
MA0002.20.0748425
MA0137.20.206905
MA0104.20.592083
MA0047.20.851978
MA0112.20.499188
MA0065.21.5262
MA0150.10.559298
MA0151.10
MA0152.10.375986
MA0153.10.311979
MA0154.10.395482
MA0155.11.93729
MA0156.10.098265
MA0157.10.111638
MA0158.10
MA0159.10.0917805
MA0160.10.32855
MA0161.10
MA0162.10.0371018
MA0163.11.51157
MA0164.10.0800163
MA0080.20.0793431
MA0018.20.069086
MA0099.20.376616
MA0079.25.778
MA0102.20.682839
MA0258.11.22775
MA0259.10.512692
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
ESR1#209984.644317478664830.0002975979808366380.00310559907280152
SUZ12#2351265.673484631441080.0006469098813635560.00530193997486686



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

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