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Coexpression cluster:C184: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:51, 17 September 2013


Full id: C184_somatostatinoma_smallcell_nonsmall_small_gastrointestinal_pineal_thyroid



Phase1 CAGE Peaks

Hg19::chr10:120200137..120200154,+p@chr10:120200137..120200154
+
Hg19::chr11:14993703..14993738,-p@chr11:14993703..14993738
-
Hg19::chr11:14993888..14993903,-p1@CALCA
Hg19::chr11:31531350..31531361,+p5@ELP4
Hg19::chr11:31531366..31531387,+p4@ELP4
Hg19::chr11:45307765..45307784,-p2@SYT13
Hg19::chr11:45307785..45307803,-p3@SYT13
Hg19::chr12:127385138..127385144,-p@chr12:127385138..127385144
-
Hg19::chr12:128045165..128045171,+p@chr12:128045165..128045171
+
Hg19::chr12:128108552..128108561,+p1@ENST00000537470
Hg19::chr12:67253036..67253040,-p@chr12:67253036..67253040
-
Hg19::chr12:70464593..70464598,+p@chr12:70464593..70464598
+
Hg19::chr12:70464652..70464662,+p@chr12:70464652..70464662
+
Hg19::chr12:70464665..70464668,+p@chr12:70464665..70464668
+
Hg19::chr12:70464675..70464680,+p@chr12:70464675..70464680
+
Hg19::chr13:110354471..110354477,-p@chr13:110354471..110354477
-
Hg19::chr13:24246893..24246939,+p@chr13:24246893..24246939
+
Hg19::chr13:93591283..93591289,-p@chr13:93591283..93591289
-
Hg19::chr13:97500658..97500682,-p@chr13:97500658..97500682
-
Hg19::chr15:59908698..59908705,+p22@GCNT3
Hg19::chr15:59908719..59908730,+p6@GCNT3
Hg19::chr15:59908741..59908754,+p12@GCNT3
Hg19::chr15:59908762..59908770,+p18@GCNT3
Hg19::chr15:59908801..59908817,+p10@GCNT3
Hg19::chr15:59908820..59908829,+p20@GCNT3
Hg19::chr15:59908955..59908965,+p16@GCNT3
Hg19::chr15:59909013..59909022,+p19@GCNT3
Hg19::chr15:59910132..59910144,+p9@GCNT3
Hg19::chr15:59910171..59910184,+p15@GCNT3
Hg19::chr15:59910206..59910219,+p17@GCNT3
Hg19::chr15:92459135..92459153,+p@chr15:92459135..92459153
+
Hg19::chr15:92459179..92459184,+p@chr15:92459179..92459184
+
Hg19::chr16:735282..735294,+p@chr16:735282..735294
+
Hg19::chr16:735529..735579,+p@chr16:735529..735579
+
Hg19::chr16:736123..736159,-p@chr16:736123..736159
-
Hg19::chr17:34037239..34037263,+p@chr17:34037239..34037263
+
Hg19::chr18:30950056..30950073,-p@chr18:30950056..30950073
-
Hg19::chr18:56813724..56813731,+p@chr18:56813724..56813731
+
Hg19::chr18:56813732..56813760,+p@chr18:56813732..56813760
+
Hg19::chr18:56815158..56815162,+p@chr18:56815158..56815162
+
Hg19::chr18:56815628..56815675,+p@chr18:56815628..56815675
+
Hg19::chr18:56815879..56815901,+p@chr18:56815879..56815901
+
Hg19::chr18:7955176..7955183,+p@chr18:7955176..7955183
+
Hg19::chr18:7955199..7955220,+p@chr18:7955199..7955220
+
Hg19::chr18:7955240..7955261,+p@chr18:7955240..7955261
+
Hg19::chr18:7955271..7955280,+p@chr18:7955271..7955280
+
Hg19::chr18:7955315..7955339,+p@chr18:7955315..7955339
+
Hg19::chr19:7570269..7570273,+p13@C19orf45
Hg19::chr19:7570395..7570427,+p5@C19orf45
Hg19::chr1:110661599..110661609,-p@chr1:110661599..110661609
-
Hg19::chr1:110678110..110678115,+p@chr1:110678110..110678115
+
Hg19::chr1:110678156..110678168,+p@chr1:110678156..110678168
+
Hg19::chr1:110678228..110678236,+p@chr1:110678228..110678236
+
Hg19::chr1:155954237..155954260,-p@chr1:155954237..155954260
-
Hg19::chr1:155954270..155954294,-p@chr1:155954270..155954294
-
Hg19::chr1:155954306..155954320,-p@chr1:155954306..155954320
-
Hg19::chr1:155954331..155954340,-p@chr1:155954331..155954340
-
Hg19::chr1:193186112..193186120,-p@chr1:193186112..193186120
-
Hg19::chr1:193186161..193186169,-p@chr1:193186161..193186169
-
Hg19::chr1:193186195..193186210,-p@chr1:193186195..193186210
-
Hg19::chr1:193232079..193232084,+p@chr1:193232079..193232084
+
Hg19::chr1:193232096..193232117,+p@chr1:193232096..193232117
+
Hg19::chr1:193232144..193232147,+p@chr1:193232144..193232147
+
Hg19::chr1:55446510..55446545,+p4@TMEM61
Hg19::chr1:6534313..6534324,-p@chr1:6534313..6534324
-
Hg19::chr20:20173664..20173680,+p@chr20:20173664..20173680
+
Hg19::chr20:401500..401515,+p@chr20:401500..401515
+
Hg19::chr20:401531..401574,+p@chr20:401531..401574
+
Hg19::chr2:42182201..42182213,-p@chr2:42182201..42182213
-
Hg19::chr2:42182357..42182372,+p@chr2:42182357..42182372
+
Hg19::chr2:8712183..8712192,-p@chr2:8712183..8712192
-
Hg19::chr4:139208173..139208199,-p@chr4:139208173..139208199
-
Hg19::chr4:173014804..173014812,+p@chr4:173014804..173014812
+
Hg19::chr4:39034552..39034578,-p4@TMEM156
Hg19::chr4:59982412..59982425,+p@chr4:59982412..59982425
+
Hg19::chr6:107596741..107596750,+p@chr6:107596741..107596750
+
Hg19::chr6:107596755..107596774,+p@chr6:107596755..107596774
+
Hg19::chr6:137243349..137243360,+p3@SLC35D3
Hg19::chr6:137243373..137243391,+p1@SLC35D3
Hg19::chr6:154858221..154858224,-p@chr6:154858221..154858224
-
Hg19::chr6:154858237..154858245,-p@chr6:154858237..154858245
-
Hg19::chr6:161970049..161970057,-p3@GU361471
Hg19::chr6:48078977..48078989,-p5@C6orf138
Hg19::chr6:50692227..50692236,+p@chr6:50692227..50692236
+
Hg19::chr6:50692244..50692251,+p@chr6:50692244..50692251
+
Hg19::chr7:129330290..129330300,+p@chr7:129330290..129330300
+
Hg19::chr8:10004983..10005007,-p@chr8:10004983..10005007
-
Hg19::chr9:77257424..77257435,-p@chr9:77257424..77257435
-
Hg19::chr9:77257468..77257474,-p@chr9:77257468..77257474
-
Hg19::chr9:77257481..77257492,-p@chr9:77257481..77257492
-
Hg19::chr9:77257683..77257703,+p@chr9:77257683..77257703
+
Hg19::chr9:96678236..96678246,-p@chr9:96678236..96678246
-


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:0031716calcitonin receptor binding0.0137489753507221
GO:0033588Elongator holoenzyme complex0.0137489753507221
GO:0001984vasodilation of artery during baroreceptor response to increased systemic arterial blood pressure0.0137489753507221
GO:0001983baroreceptor response to increased systemic arterial blood pressure0.0137489753507221
GO:0003829beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity0.0137489753507221
GO:0050961detection of temperature stimulus during sensory perception0.0137489753507221
GO:0045932negative regulation of muscle contraction0.0137489753507221
GO:0050965detection of temperature stimulus during sensory perception of pain0.0137489753507221
GO:0045986negative regulation of smooth muscle contraction0.0137489753507221
GO:0043195terminal button0.0137489753507221
GO:0004406H3/H4 histone acetyltransferase activity0.0137489753507221
GO:0008109N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity0.0137489753507221
GO:0001978carotid sinus baroreceptor feedback regulation of systemic arterial blood pressure0.0137489753507221
GO:0033267axon part0.0137489753507221
GO:0016048detection of temperature stimulus0.0137489753507221
GO:0050951sensory perception of temperature stimulus0.0137489753507221
GO:0003025baroreceptor regulation of systemic arterial blood pressure0.0137489753507221
GO:0016021integral to membrane0.0137489753507221
GO:0031224intrinsic to membrane0.0137489753507221
GO:0048265response to pain0.0137489753507221
GO:0003085negative regulation of systemic arterial blood pressure0.0137489753507221
GO:0008607phosphorylase kinase regulator activity0.0137489753507221
GO:0002027regulation of heart rate0.0139590597962431
GO:0051482elevation of cytosolic calcium ion concentration during G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0139590597962431
GO:0045778positive regulation of ossification0.0139590597962431
GO:0016944RNA polymerase II transcription elongation factor activity0.0139590597962431
GO:0031645negative regulation of neurological process0.0151207568562064
GO:0046852positive regulation of bone remodeling0.0151207568562064
GO:0001976regulation of systemic arterial blood pressure by neurological process0.0156069152171386
GO:0045776negative regulation of blood pressure0.0156069152171386
GO:0030279negative regulation of ossification0.0156069152171386
GO:0044425membrane part0.0201527026644171
GO:0046851negative regulation of bone remodeling0.0201527026644171
GO:0033555multicellular organismal response to stress0.0207263588466125
GO:0008023transcription elongation factor complex0.0207263588466125
GO:0009408response to heat0.0218275968006529
GO:0019233sensory perception of pain0.0244999460665658
GO:0007202phospholipase C activation0.0247905539309607
GO:0003073regulation of systemic arterial blood pressure0.0247905539309607
GO:0003711transcription elongation regulator activity0.0271865372509221
GO:0042311vasodilation0.0273275662456433
GO:0030278regulation of ossification0.0273275662456433
GO:0006940regulation of smooth muscle contraction0.0280939917086146
GO:0007190adenylate cyclase activation0.0301823823024857
GO:0046850regulation of bone remodeling0.0301823823024857
GO:0051241negative regulation of multicellular organismal process0.0301823823024857
GO:0031644regulation of neurological process0.0301823823024857
GO:0004468lysine N-acetyltransferase activity0.0301823823024857
GO:0004402histone acetyltransferase activity0.0301823823024857
GO:0051349positive regulation of lyase activity0.0301823823024857
GO:0045762positive regulation of adenylate cyclase activity0.0301823823024857
GO:0031281positive regulation of cyclase activity0.0301823823024857
GO:0009266response to temperature stimulus0.0330195727456264
GO:0006493protein amino acid O-linked glycosylation0.0335221671514171
GO:0030424axon0.0372856665626736
GO:0043025cell soma0.0376930235471054
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0377782978616244
GO:0007631feeding behavior0.0377782978616244
GO:0016020membrane0.0377782978616244
GO:0006937regulation of muscle contraction0.0377782978616244
GO:0006939smooth muscle contraction0.0377782978616244
GO:0045761regulation of adenylate cyclase activity0.0377782978616244
GO:0031279regulation of cyclase activity0.0377782978616244
GO:0035150regulation of tube size0.0377782978616244
GO:0050880regulation of blood vessel size0.0377782978616244
GO:0051339regulation of lyase activity0.0377782978616244
GO:0008016regulation of heart contraction0.0377782978616244
GO:0003018vascular process in circulatory system0.0381050662887932
GO:0008375acetylglucosaminyltransferase activity0.0382569587600429
GO:0009582detection of abiotic stimulus0.0382569587600429
GO:0050906detection of stimulus during sensory perception0.0382569587600429
GO:0003015heart process0.0382569587600429
GO:0044463cell projection part0.0382569587600429
GO:0060047heart contraction0.0382569587600429
GO:0009581detection of external stimulus0.0401438385172046
GO:0008217regulation of blood pressure0.0435547660791225
GO:0030133transport vesicle0.0492015448315908



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><br>disease_data<br>

Disease
Ontology termp-valuen
somatostatinoma1.23e-661
lung small cell carcinoma1.03e-174
neuroendocrine tumor2.19e-126
bronchus cancer9.89e-117
bronchogenic carcinoma9.89e-117
lung carcinoma1.21e-089
neuroectodermal tumor5.73e-0810


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)
MA0003.12.92366e-08
MA0004.10.059644
MA0006.10.0188876
MA0007.10.800602
MA0009.10.731476
MA0014.10.0112454
MA0017.10.385198
MA0019.10.192717
MA0024.10.068993
MA0025.10.183196
MA0027.11.47809
MA0028.10.00823259
MA0029.10.0761517
MA0030.11.89858
MA0031.13.30935
MA0038.10.0522657
MA0040.10.078397
MA0041.10.295713
MA0042.10.0518809
MA0043.10.732147
MA0046.10.348554
MA0048.10.879104
MA0050.10.122838
MA0051.10.138532
MA0052.10.0799011
MA0055.13.46397
MA0056.10
MA0057.10.100506
MA0058.10.106926
MA0059.10.0180581
MA0060.10.38269
MA0061.10.0416603
MA0063.10
MA0066.11.43766
MA0067.10.304116
MA0068.17.09603e-05
MA0069.10.700363
MA0070.10.677051
MA0071.10.225678
MA0072.10.667761
MA0073.10.314682
MA0074.11.40684
MA0076.10.127077
MA0077.11.08532
MA0078.11.13094
MA0081.10.192975
MA0083.10.371099
MA0084.10.448027
MA0087.10.32237
MA0088.10.561366
MA0089.10
MA0090.10.00771878
MA0091.12.31628
MA0092.10.982407
MA0093.10.0199133
MA0095.10
MA0098.10
MA0100.10.534027
MA0101.10.176497
MA0103.11.66607
MA0105.10.00408927
MA0106.10.913841
MA0107.10.0612513
MA0108.20.185137
MA0109.10
MA0111.10.289689
MA0113.10.207971
MA0114.10.250917
MA0115.10.251028
MA0116.10.032712
MA0117.10.130757
MA0119.10.412433
MA0122.10.443081
MA0124.10.223844
MA0125.10.172798
MA0130.10
MA0131.10.0282896
MA0132.10
MA0133.10
MA0135.10.127133
MA0136.10.150065
MA0139.10.0900265
MA0140.10.0359282
MA0141.10.103316
MA0142.10.160036
MA0143.10.20819
MA0144.10.0787341
MA0145.10.847926
MA0146.14.36987e-05
MA0147.10.000273782
MA0148.14.55701
MA0149.10.00598841
MA0062.20.0188104
MA0035.21.96299
MA0039.20.454775
MA0138.20.0248704
MA0002.20.230789
MA0137.20.123407
MA0104.20.00103717
MA0047.23.5947
MA0112.20.743124
MA0065.20.642209
MA0150.10.24544
MA0151.10
MA0152.10.0382624
MA0153.10.163249
MA0154.10.023977
MA0155.10.0669785
MA0156.10.674539
MA0157.12.29584
MA0158.10
MA0159.10.0698723
MA0160.10.190068
MA0161.10
MA0162.13.97932e-07
MA0163.10.00260989
MA0164.10.427436
MA0080.20.402771
MA0018.21.27739
MA0099.20.110132
MA0079.20.00022845
MA0102.20.478533
MA0258.10.653631
MA0259.10.323807
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#209993.009972061580330.003090122978166250.0162871235789405
NR3C1#2908132.115753296796190.008118307284096510.0320615577403576



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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