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Coexpression cluster:C249

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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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
central nervous system1.00e-2882
regional part of nervous system3.24e-2894
nervous system3.24e-2894
tube3.24e-27194
neural tube5.44e-2757
neural rod5.44e-2757
future spinal cord5.44e-2757
neural keel5.44e-2757
brain5.95e-2469
future brain5.95e-2469
regional part of brain7.48e-2359
anatomical conduit3.37e-21241
epithelium2.17e-20309
cell layer9.46e-20312
anterior neural tube1.80e-1942
regional part of forebrain2.45e-1941
forebrain2.45e-1941
future forebrain2.45e-1941
neurectoderm4.25e-1990
multi-tissue structure7.33e-19347
neural plate9.52e-1886
presumptive neural plate9.52e-1886
organism subdivision3.57e-17365
gray matter8.53e-1734
brain grey matter8.53e-1734
cerebral hemisphere1.27e-1632
telencephalon1.34e-1634
adult organism5.55e-16115
regional part of telencephalon5.95e-1633
anatomical cluster1.44e-15286
regional part of cerebral cortex6.54e-1522
cerebral cortex3.23e-1425
pallium3.23e-1425
neocortex6.45e-1420
organ part1.15e-13219
pre-chordal neural plate6.25e-1361
ectoderm4.68e-11173
presumptive ectoderm4.68e-11173
ectoderm-derived structure4.31e-10169
head6.22e-10123
embryo6.68e-10612
anterior region of body9.45e-10129
craniocervical region9.45e-10129
subdivision of trunk4.19e-09113
cavitated compound organ1.04e-0832
posterior neural tube1.08e-0815
chordal neural plate1.08e-0815
embryonic structure3.22e-08605
developing anatomical structure3.22e-08605
trunk5.15e-08216
trunk region element5.57e-08107
germ layer5.58e-08604
embryonic tissue5.58e-08604
presumptive structure5.58e-08604
epiblast (generic)5.58e-08604
duct9.23e-0826
immaterial anatomical entity1.20e-07126
kidney1.54e-0727
kidney mesenchyme1.54e-0727
kidney rudiment1.54e-0727
kidney field1.54e-0727
multi-cellular organism3.18e-07659
segmental subdivision of nervous system3.75e-0713
segmental subdivision of hindbrain5.29e-0712
hindbrain5.29e-0712
presumptive hindbrain5.29e-0712
anatomical space5.61e-07104
abdominal segment of trunk7.74e-0761
abdomen7.74e-0761
mesonephros7.84e-0718
pronephros7.84e-0718
nephrogenic cord7.84e-0718
pronephric mesoderm7.84e-0718
rostral part of nephrogenic cord7.84e-0718
presumptive pronephric mesoderm7.84e-0718
Disease
Ontology termp-valuen
cell type cancer6.64e-08143


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)

{{{tfbs_overrepresentation_jaspar}}}



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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