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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 10:39, 17 September 2013


Full id: C135_neuroblastoma_retinoblastoma_carcinoid_choriocarcinoma_testicular_acute_rectum



Phase1 CAGE Peaks

Hg19::chr10:135139802..135139811,-p9@CALY
Hg19::chr11:71952706..71952712,-p4@PHOX2A
Hg19::chr11:71952721..71952728,-p6@PHOX2A
Hg19::chr11:71952772..71952788,-p@chr11:71952772..71952788
-
Hg19::chr11:71955210..71955227,-p1@PHOX2A
Hg19::chr11:72070206..72070217,-p@chr11:72070206..72070217
-
Hg19::chr11:8285219..8285232,-p8@LMO1
Hg19::chr14:36003132..36003155,-p@chr14:36003132..36003155
-
Hg19::chr14:36003180..36003191,-p@chr14:36003180..36003191
-
Hg19::chr14:36003234..36003238,-p@chr14:36003234..36003238
-
Hg19::chr14:36003363..36003378,+p1@INSM2
Hg19::chr14:36003405..36003408,+p3@INSM2
Hg19::chr14:89307203..89307210,+p5@TTC8
Hg19::chr14:89307222..89307227,+p7@TTC8
Hg19::chr14:89307231..89307234,+p8@TTC8
Hg19::chr14:89307240..89307249,+p4@TTC8
Hg19::chr14:89319304..89319352,+p@chr14:89319304..89319352
+
Hg19::chr16:55689872..55689912,+p1@SLC6A2
Hg19::chr17:61509320..61509322,-p@chr17:61509320..61509322
-
Hg19::chr19:30719524..30719534,+p@chr19:30719524..30719534
+
Hg19::chr1:109255524..109255546,+p1@FNDC7
Hg19::chr1:99470368..99470446,-p1@LPPR5
Hg19::chr20:21086993..21087007,-p1@LINC00237
Hg19::chr22:45405796..45405814,-p3@PHF21B
Hg19::chr2:137522983..137523027,+p4@THSD7B
Hg19::chr2:16080165..16080175,+p15@MYCN
Hg19::chr2:16080325..16080331,+p17@MYCN
Hg19::chr2:16080357..16080363,+p18@MYCN
Hg19::chr2:16080460..16080495,-p@chr2:16080460..16080495
-
Hg19::chr2:16080635..16080650,+p4@MYCN
Hg19::chr2:16080659..16080685,+p1@MYCN
Hg19::chr2:16080823..16080836,+p5@MYCN
Hg19::chr2:16081024..16081034,+p10@MYCN
Hg19::chr2:16081392..16081406,-p3@MYCNOS
Hg19::chr2:16081716..16081740,-p2@MYCNOS
Hg19::chr2:16081744..16081768,-p5@MYCNOS
Hg19::chr2:16081783..16081817,-p1@MYCNOS
Hg19::chr2:16081912..16081931,+p2@MYCN
Hg19::chr2:16082094..16082106,+p7@MYCN
Hg19::chr2:16082155..16082169,+p3@MYCN
Hg19::chr2:16082384..16082391,+p9@MYCN
Hg19::chr2:16082395..16082415,+p6@MYCN
Hg19::chr2:16082418..16082429,+p8@MYCN
Hg19::chr2:16082486..16082491,+p13@MYCN
Hg19::chr2:16082851..16082860,+p@chr2:16082851..16082860
+
Hg19::chr2:16082878..16082890,+p@chr2:16082878..16082890
+
Hg19::chr2:16082902..16082908,+p@chr2:16082902..16082908
+
Hg19::chr2:16082933..16082942,+p@chr2:16082933..16082942
+
Hg19::chr2:16083539..16083543,+p@chr2:16083539..16083543
+
Hg19::chr2:16085596..16085604,+p@chr2:16085596..16085604
+
Hg19::chr2:16085699..16085709,+p@chr2:16085699..16085709
+
Hg19::chr2:16085756..16085766,+p@chr2:16085756..16085766
+
Hg19::chr2:16085836..16085841,-p@chr2:16085836..16085841
-
Hg19::chr2:16085862..16085895,-p@chr2:16085862..16085895
-
Hg19::chr2:16085916..16085937,-p@chr2:16085916..16085937
-
Hg19::chr2:16122765..16122769,-p@chr2:16122765..16122769
-
Hg19::chr2:16361177..16361195,-p@chr2:16361177..16361195
-
Hg19::chr2:16383015..16383029,-p@chr2:16383015..16383029
-
Hg19::chr2:16405283..16405330,+p1@ENST00000420404
Hg19::chr2:16504184..16504211,+p@chr2:16504184..16504211
+
Hg19::chr2:173724826..173724840,+p15@RAPGEF4
Hg19::chr2:173724864..173724875,+p11@RAPGEF4
Hg19::chr2:173724876..173724893,+p16@RAPGEF4
Hg19::chr2:192364133..192364143,+p@chr2:192364133..192364143
+
Hg19::chr2:30099704..30099722,-p@chr2:30099704..30099722
-
Hg19::chr2:30099741..30099749,-p@chr2:30099741..30099749
-
Hg19::chr2:74726898..74726903,+p@chr2:74726898..74726903
+
Hg19::chr2:74735271..74735288,-p10@PCGF1
Hg19::chr2:74735290..74735299,-p11@PCGF1
Hg19::chr2:74735317..74735338,-p5@PCGF1
Hg19::chr2:74740569..74740580,+p4@TLX2
Hg19::chr2:74741569..74741620,+p1@TLX2
Hg19::chr2:74743961..74743965,+p@chr2:74743961..74743965
+
Hg19::chr4:113869733..113869760,+p@chr4:113869733..113869760
+
Hg19::chr4:113870230..113870237,+p@chr4:113870230..113870237
+
Hg19::chr4:151509442..151509449,-p@chr4:151509442..151509449
-
Hg19::chr4:151509505..151509510,-p@chr4:151509505..151509510
-
Hg19::chr4:151509549..151509560,-p@chr4:151509549..151509560
-
Hg19::chr4:151509603..151509613,-p@chr4:151509603..151509613
-
Hg19::chr4:151509614..151509615,-p@chr4:151509614..151509615
-
Hg19::chr4:151509622..151509629,-p@chr4:151509622..151509629
-
Hg19::chr4:174427862..174427899,+p@chr4:174427862..174427899
+
Hg19::chr4:174429225..174429237,+p@chr4:174429225..174429237
+
Hg19::chr4:174429255..174429289,+p@chr4:174429255..174429289
+
Hg19::chr4:174429652..174429665,+p@chr4:174429652..174429665
+
Hg19::chr4:174440390..174440400,-p@chr4:174440390..174440400
-
Hg19::chr4:174440405..174440414,-p@chr4:174440405..174440414
-
Hg19::chr4:174930472..174930480,-p@chr4:174930472..174930480
-
Hg19::chr4:174930493..174930503,-p@chr4:174930493..174930503
-
Hg19::chr4:174930547..174930558,-p@chr4:174930547..174930558
-
Hg19::chr4:175028534..175028537,-p@chr4:175028534..175028537
-
Hg19::chr4:175041663..175041727,-p1@ENST00000503140
Hg19::chr4:21699314..21699327,-p7@KCNIP4
Hg19::chr4:21699348..21699355,-p25@KCNIP4
Hg19::chr4:21699357..21699368,-p18@KCNIP4
Hg19::chr4:21699380..21699386,-p20@KCNIP4
Hg19::chr4:41859832..41859854,+p@chr4:41859832..41859854
+
Hg19::chr4:41875797..41875802,-p@chr4:41875797..41875802
-
Hg19::chr4:41884582..41884593,-p1@ENST00000499082
Hg19::chr4:41884620..41884663,-p1@ENST00000504870
Hg19::chr4:48485220..48485230,+p10@SLC10A4
Hg19::chr4:48485239..48485249,+p9@SLC10A4
Hg19::chr4:48485341..48485394,+p1@SLC10A4
Hg19::chr4:48485400..48485411,+p3@SLC10A4
Hg19::chr4:48485413..48485423,+p5@SLC10A4
Hg19::chr4:48485436..48485441,+p12@SLC10A4
Hg19::chr4:48485486..48485499,+p2@SLC10A4
Hg19::chr4:95983128..95983134,+p@chr4:95983128..95983134
+
Hg19::chr5:168271822..168271868,-p5@SLIT3
Hg19::chr5:168271880..168271889,-p15@SLIT3
Hg19::chr5:50761081..50761087,-p@chr5:50761081..50761087
-
Hg19::chr5:51202170..51202198,+p@chr5:51202170..51202198
+
Hg19::chr6:154360476..154360504,+p2@OPRM1
Hg19::chr6:154360522..154360525,+p14@OPRM1
Hg19::chr6:154360530..154360549,+p3@OPRM1
Hg19::chr6:154360553..154360567,+p4@OPRM1
Hg19::chr7:133694696..133694724,+p16@EXOC4
Hg19::chr7:19185493..19185503,-p2@FERD3L
Hg19::chr7:73919759..73919766,-p@chr7:73919759..73919766
-
Hg19::chr7:73919790..73919798,-p@chr7:73919790..73919798
-
Hg19::chr7:73919799..73919805,-p@chr7:73919799..73919805
-
Hg19::chr7:8276508..8276551,-p14@ICA1
Hg19::chr7:8276855..8276873,+p@chr7:8276855..8276873
+
Hg19::chr7:8301962..8301966,-p17@ICA1
Hg19::chr7:8301975..8301984,-p11@ICA1
Hg19::chr7:8301994..8301997,-p19@ICA1
Hg19::chr7:8302002..8302015,-p10@ICA1
Hg19::chr7:8302097..8302104,-p15@ICA1
Hg19::chr7:8302126..8302136,-p12@ICA1
Hg19::chr7:8302298..8302323,-p9@ICA1
Hg19::chr8:13373093..13373105,-p55@DLC1
Hg19::chr8:142878006..142878015,+p@chr8:142878006..142878015
+
Hg19::chr8:73164078..73164082,-p6@LOC392232
Hg19::chr9:136501478..136501491,+p1@DBH
Hg19::chr9:137605204..137605213,+p@chr9:137605204..137605213
+


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:0032989cellular structure morphogenesis0.012351859015746
GO:0000902cell morphogenesis0.012351859015746
GO:0032501multicellular organismal process0.012351859015746
GO:0030141secretory granule0.012351859015746
GO:0032990cell part morphogenesis0.012351859015746
GO:0048858cell projection morphogenesis0.012351859015746
GO:0030030cell projection organization and biogenesis0.012351859015746
GO:0005333norepinephrine transmembrane transporter activity0.0185446838572942
GO:0005334norephinephrine:sodium symporter activity0.0185446838572942
GO:0042583chromaffin granule0.0185446838572942
GO:0015874norepinephrine transport0.0185446838572942
GO:0007268synaptic transmission0.0200921373067378
GO:0050877neurological system process0.0226023037666984
GO:0019226transmission of nerve impulse0.0233722017898953
GO:0006836neurotransmitter transport0.0233722017898953
GO:0009914hormone transport0.023991938083013
GO:0050774negative regulation of dendrite morphogenesis0.023991938083013
GO:0015370solute:sodium symporter activity0.0247353766381847
GO:0048814regulation of dendrite morphogenesis0.0291244924816904
GO:0004988mu-opioid receptor activity0.0291244924816904
GO:0030672synaptic vesicle membrane0.0291244924816904
GO:0003008system process0.0293082164144434
GO:0006887exocytosis0.0293082164144434
GO:0015294solute:cation symporter activity0.0293082164144434
GO:0050773regulation of dendrite development0.0293082164144434
GO:0048813dendrite morphogenesis0.0293082164144434
GO:0048667neuron morphogenesis during differentiation0.0293082164144434
GO:0048812neurite morphogenesis0.0293082164144434
GO:0000904cellular morphogenesis during differentiation0.0311410238356019
GO:0032502developmental process0.0313272232327204
GO:0048265response to pain0.0313272232327204
GO:0008504monoamine transmembrane transporter activity0.0313272232327204
GO:0031175neurite development0.0313272232327204
GO:0009653anatomical structure morphogenesis0.0342713320105026
GO:0015844monoamine transport0.0349185433074233
GO:0048666neuron development0.0371398780115165
GO:0030667secretory granule membrane0.0385248908208417
GO:0008508bile acid:sodium symporter activity0.0417582874367942
GO:0004500dopamine beta-monooxygenase activity0.0417582874367942
GO:0042423catecholamine biosynthetic process0.0496224120078445
GO:0015125bile acid transmembrane transporter activity0.0496224120078445



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
migratory neural crest cell7.46e-1541
neurectodermal cell8.52e-1159
ectodermal cell4.40e-0972
Uber Anatomy
Ontology termp-valuen
sympathetic nervous system7.76e-1185
autonomic nervous system7.76e-1185
peripheral nervous system3.75e-668
nervous system1.68e-0789
Disease
Ontology termp-valuen
neuroendocrine tumor1.83e-986
neuroectodermal tumor1.10e-5910
germ cell and embryonal cancer7.08e-2822
germ cell cancer7.08e-2822


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)
MA0003.10.935339
MA0004.10.702631
MA0006.10.204923
MA0007.10.613349
MA0009.10.0527449
MA0014.10.799953
MA0017.10.0241642
MA0019.11.5733
MA0024.11.60189
MA0025.10.101845
MA0027.11.31495
MA0028.10.0151535
MA0029.10.871761
MA0030.10.0284071
MA0031.10.200597
MA0038.10.0409271
MA0040.10.563389
MA0041.10.00346285
MA0042.10.200982
MA0043.10.195702
MA0046.10.730311
MA0048.10.154744
MA0050.10.00197975
MA0051.10.00171201
MA0052.10.13318
MA0055.10.00445706
MA0056.10
MA0057.10.417572
MA0058.11.18897
MA0059.14.15075
MA0060.10.00174732
MA0061.11.82927
MA0063.10
MA0066.10.331888
MA0067.10.1975
MA0068.11.85609
MA0069.10.182323
MA0070.10.172692
MA0071.10.57208
MA0072.10.0440847
MA0073.10.032489
MA0074.10.187008
MA0076.10.00829244
MA0077.10.162496
MA0078.10.0987698
MA0081.10.303945
MA0083.10.0550275
MA0084.10.322179
MA0087.10.675015
MA0088.10.73236
MA0089.10
MA0090.10.28835
MA0091.10.362464
MA0092.10.938699
MA0093.11.54445
MA0095.10
MA0098.10
MA0100.10.217422
MA0101.10.0525197
MA0103.10.116497
MA0105.12.68212
MA0106.12.76944
MA0107.10.0639688
MA0108.20.197037
MA0109.10
MA0111.10.638963
MA0113.10.297751
MA0114.10.0035465
MA0115.10.15414
MA0116.10.319528
MA0117.10.0647513
MA0119.10.00108258
MA0122.10.0738617
MA0124.10.132703
MA0125.10.646619
MA0130.10
MA0131.10.417972
MA0132.10
MA0133.10
MA0135.10.838367
MA0136.10.0441433
MA0139.10.0428546
MA0140.11.31664
MA0141.10.0707555
MA0142.10.837237
MA0143.10.987252
MA0144.10.221909
MA0145.10.742022
MA0146.10.517416
MA0147.10.336196
MA0148.10.286382
MA0149.10.0588167
MA0062.20.00106062
MA0035.20.134588
MA0039.20.23779
MA0138.20.379162
MA0002.20.0605037
MA0137.21.51588
MA0104.20.170554
MA0047.20.854008
MA0112.22.30115
MA0065.20.295814
MA0150.10.17511
MA0151.10
MA0152.10.253688
MA0153.11.0286
MA0154.11.63928
MA0155.10.26271
MA0156.10.0722037
MA0157.10.137895
MA0158.10
MA0159.11.0558
MA0160.10.681338
MA0161.10
MA0162.10.259104
MA0163.12.58884
MA0164.10.0264804
MA0080.20.213905
MA0018.20.0629331
MA0099.20.0274856
MA0079.24.77068
MA0102.20.349586
MA0258.10.00867538
MA0259.10.951567
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
CTBP2#148883.71656298307130.001536855659656330.00976977711600508
EP300#2033422.107448537047221.16633482712618e-064.76009546737908e-05
GATA2#2624403.776276069201181.00033832709499e-131.56868370185396e-11
RAD21#5885231.764190959966630.005193286834045140.0240694809470507
REST#5978292.072969131612690.0001132853343542980.00155165993896767



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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