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

Latest revision as of 10:44, 17 September 2013


Full id: C155_pituitary_placenta_nonsmall_cervical_smallcell_choriocarcinoma_epitheloid



Phase1 CAGE Peaks

Hg19::chr10:124615386..124615429,-p@chr10:124615386..124615429
-
Hg19::chr11:30252514..30252529,+p4@FSHB
Hg19::chr11:30252549..30252565,+p1@FSHB
Hg19::chr11:46295968..46295985,-p1@ENST00000527239
Hg19::chr11:70178863..70178874,+p@chr11:70178863..70178874
+
Hg19::chr12:7341800..7341812,+p5@PEX5
Hg19::chr13:78813679..78813681,-p@chr13:78813679..78813681
-
Hg19::chr14:101193418..101193423,+p8@DLK1
Hg19::chr16:60564560..60564561,+p@chr16:60564560..60564561
+
Hg19::chr17:18012035..18012048,+p2@MYO15A
Hg19::chr17:185919..185925,-p@chr17:185919..185925
-
Hg19::chr17:26877299..26877303,+p@chr17:26877299..26877303
+
Hg19::chr17:61973929..61973936,-p3@CSH1
Hg19::chr17:61994613..61994649,-p@chr17:61994613..61994649
-
Hg19::chr17:61994760..61994767,+p@chr17:61994760..61994767
+
Hg19::chr17:61994797..61994839,-p@chr17:61994797..61994839
-
Hg19::chr17:61995172..61995199,-p@chr17:61995172..61995199
-
Hg19::chr17:61995207..61995219,-p@chr17:61995207..61995219
-
Hg19::chr17:61995220..61995244,-p@chr17:61995220..61995244
-
Hg19::chr17:61995371..61995384,+p@chr17:61995371..61995384
+
Hg19::chr17:61995410..61995414,-p@chr17:61995410..61995414
-
Hg19::chr17:61995432..61995458,-p@chr17:61995432..61995458
-
Hg19::chr17:61995480..61995499,-p@chr17:61995480..61995499
-
Hg19::chr17:61995704..61995739,+p@chr17:61995704..61995739
+
Hg19::chr17:61995740..61995772,-p1@AB591020
Hg19::chr17:61996192..61996199,-p1@GH1
p2@CSHL1
Hg19::chr17:76919498..76919500,+p@chr17:76919498..76919500
+
Hg19::chr18:13915530..13915540,-p1@MC2R
Hg19::chr19:4769143..4769147,+p1@MIR7-3HG
Hg19::chr19:4772190..4772197,+p@chr19:4772190..4772197
+
Hg19::chr19:49519347..49519354,-p3@CU678753
Hg19::chr19:49519357..49519372,-p1@CU678753
Hg19::chr19:49519519..49519562,-p2@CU678753
Hg19::chr19:49519930..49519937,-p@chr19:49519930..49519937
-
Hg19::chr19:49520344..49520367,-p1@LHB
Hg19::chr19:49547457..49547458,+p2@CGB5
Hg19::chr19:7979644..7979653,+p@chr19:7979644..7979653
+
Hg19::chr19:7979665..7979675,+p@chr19:7979665..7979675
+
Hg19::chr19:7979677..7979703,+p@chr19:7979677..7979703
+
Hg19::chr19:7979708..7979734,+p@chr19:7979708..7979734
+
Hg19::chr1:115572444..115572451,+p1@TSHB
Hg19::chr1:151696600..151696645,+p@chr1:151696600..151696645
+
Hg19::chr1:19435681..19435684,+p@chr1:19435681..19435684
+
Hg19::chr1:2036352..2036358,-p@chr1:2036352..2036358
-
Hg19::chr1:233598660..233598662,-p@chr1:233598660..233598662
-
Hg19::chr1:240043364..240043366,+p@chr1:240043364..240043366
+
Hg19::chr1:65990750..65990756,+p@chr1:65990750..65990756
+
Hg19::chr20:19714764..19714765,+p@chr20:19714764..19714765
+
Hg19::chr20:33567825..33567827,-p@chr20:33567825..33567827
-
Hg19::chr20:36511296..36511298,+p@chr20:36511296..36511298
+
Hg19::chr20:5903139..5903148,+p@chr20:5903139..5903148
+
Hg19::chr20:5903320..5903383,-p@chr20:5903320..5903383
-
Hg19::chr22:19373363..19373368,+p@chr22:19373363..19373368
+
Hg19::chr22:47126639..47126654,+p@chr22:47126639..47126654
+
Hg19::chr2:175434561..175434564,+p@chr2:175434561..175434564
+
Hg19::chr2:193063406..193063411,-p@chr2:193063406..193063411
-
Hg19::chr2:241080069..241080082,-p1@OTOS
Hg19::chr2:863855..863859,-p2@ENST00000415700
p2@uc002qwn.1
p2@uc002qwo.1
Hg19::chr2:863883..863897,-p1@ENST00000415700
p1@uc002qwn.1
p1@uc002qwo.1
Hg19::chr3:187654553..187654555,+p@chr3:187654553..187654555
+
Hg19::chr3:53894448..53894449,+p@chr3:53894448..53894449
+
Hg19::chr3:56445982..56445989,+p@chr3:56445982..56445989
+
Hg19::chr4:166300084..166300091,+p8@CPE
Hg19::chr4:68620100..68620112,-p1@GNRHR
Hg19::chr5:462101..462128,+p8@EXOC3
Hg19::chr5:79375654..79375674,+p@chr5:79375654..79375674
+
Hg19::chr5:79375715..79375734,+p@chr5:79375715..79375734
+
Hg19::chr5:79375755..79375801,+p@chr5:79375755..79375801
+
Hg19::chr6:22287647..22287662,-p@chr6:22287647..22287662
-
Hg19::chr6:22287710..22287718,-p@chr6:22287710..22287718
-
Hg19::chr6:22287720..22287725,-p@chr6:22287720..22287725
-
Hg19::chr6:22287728..22287735,-p@chr6:22287728..22287735
-
Hg19::chr6:22287747..22287758,-p@chr6:22287747..22287758
-
Hg19::chr6:22287768..22287781,-p@chr6:22287768..22287781
-
Hg19::chr6:22287787..22287798,-p@chr6:22287787..22287798
-
Hg19::chr6:22287815..22287820,-p@chr6:22287815..22287820
-
Hg19::chr6:22290440..22290455,+p@chr6:22290440..22290455
+
Hg19::chr6:22290447..22290450,-p@chr6:22290447..22290450
-
Hg19::chr6:22290473..22290492,-p@chr6:22290473..22290492
-
Hg19::chr6:22290492..22290497,+p@chr6:22290492..22290497
+
Hg19::chr6:22290499..22290506,+p@chr6:22290499..22290506
+
Hg19::chr6:22292805..22292814,-p@chr6:22292805..22292814
-
Hg19::chr6:22292828..22292837,-p@chr6:22292828..22292837
-
Hg19::chr6:22292841..22292854,-p@chr6:22292841..22292854
-
Hg19::chr6:22294671..22294709,-p2@PRL
Hg19::chr6:22294718..22294725,-p11@PRL
Hg19::chr6:22294730..22294743,-p6@PRL
Hg19::chr6:22294755..22294768,-p9@PRL
Hg19::chr6:22294783..22294799,-p5@PRL
Hg19::chr6:22294803..22294830,-p7@PRL
Hg19::chr6:31744574..31744603,-p4@VWA7
Hg19::chr6:74072975..74072976,-p@chr6:74072975..74072976
-
Hg19::chr6:87795324..87795331,-p@chr6:87795324..87795331
-
Hg19::chr6:87795365..87795378,-p@chr6:87795365..87795378
-
Hg19::chr6:87804815..87804830,-p1@CGA
Hg19::chr7:116689..116690,+p@chr7:116689..116690
+
Hg19::chr7:130010774..130010781,-p@chr7:130010774..130010781
-
Hg19::chr7:31003593..31003614,+p2@GHRHR
Hg19::chr7:31003621..31003641,+p3@GHRHR
Hg19::chr7:31006831..31006834,+p@chr7:31006831..31006834
+
Hg19::chr8:112641680..112641681,+p@chr8:112641680..112641681
+
Hg19::chr8:126582844..126582849,-p@chr8:126582844..126582849
-
Hg19::chr8:143411767..143411777,+p@chr8:143411767..143411777
+
Hg19::chr9:75733141..75733143,+p@chr9:75733141..75733143
+
Hg19::chr9:92757667..92757670,+p@chr9:92757667..92757670
+
Hg19::chrX:103145056..103145060,+p@chrX:103145056..103145060
+
Hg19::chrX:130215564..130215579,+p@chrX:130215564..130215579
+
Hg19::chrX:130423225..130423228,-p5@IGSF1
Hg19::chrX:45029527..45029529,-p@chrX:45029527..45029529
-
Hg19::chrX:48689717..48689744,-p@chrX:48689717..48689744
-
Hg19::chrX:54051809..54051811,+p@chrX:54051809..54051811
+


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
1.28980561285789e-148.16446952939045e-129272Neuroactive ligand-receptor interaction (KEGG):04080
3.39083674685837e-070.0001073199830380674101GnRH signaling pathway (KEGG):04912
0.0004690548717164540.0494852889660859254Autoimmune thyroid disease (KEGG):05320
5.64655121093405e-070.0001191422305507087932Signaling by GPCR (Reactome):REACT_14797
4.68717995579227e-060.0005933969824033024195Metabolism of amino acids and derivatives (Reactome):REACT_13
2.72912932716038e-060.000431884716023136733{ARRB2,743} (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:0005179hormone activity4.70217539406628e-06
GO:0005625soluble fraction4.70217539406628e-06
GO:0007165signal transduction0.000669354161378072
GO:0007154cell communication0.00102865316074998
GO:0008584male gonad development0.00116701178172978
GO:0000267cell fraction0.00116701178172978
GO:0046546development of primary male sexual characteristics0.00170211124438285
GO:0005102receptor binding0.00170211124438285
GO:0032501multicellular organismal process0.00195375485702507
GO:0046661male sex differentiation0.00199734198145008
GO:0008406gonad development0.00406384487868871
GO:0048608reproductive structure development0.00406384487868871
GO:0007275multicellular organismal development0.00406384487868871
GO:0032502developmental process0.00406384487868871
GO:0022414reproductive process0.00406384487868871
GO:0045137development of primary sexual characteristics0.00406384487868871
GO:0048609reproductive process in a multicellular organism0.00406384487868871
GO:0032504multicellular organism reproduction0.00406384487868871
GO:0007166cell surface receptor linked signal transduction0.00410264335334982
GO:0030070insulin processing0.00410264335334982
GO:0004978adrenocorticotropin receptor activity0.00410264335334982
GO:0016913follicle-stimulating hormone activity0.00410264335334982
GO:0004183carboxypeptidase E activity0.00410264335334982
GO:0048187inhibin beta-B binding0.00410264335334982
GO:0007186G-protein coupled receptor protein signaling pathway0.00477227000525781
GO:0007565female pregnancy0.00477227000525781
GO:0007548sex differentiation0.00477227000525781
GO:0003006reproductive developmental process0.00530528956091789
GO:0048186inhibin beta-A binding0.00656287675267367
GO:0005148prolactin receptor binding0.00656287675267367
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.00820190560634466
GO:0048513organ development0.00820190560634466
GO:0048856anatomical structure development0.00820190560634466
GO:0019935cyclic-nucleotide-mediated signaling0.00820190560634466
GO:0004968gonadotropin-releasing hormone receptor activity0.00820190560634466
GO:0060011Sertoli cell proliferation0.00820190560634466
GO:0050954sensory perception of mechanical stimulus0.00893161013195159
GO:0007605sensory perception of sound0.00893161013195159
GO:0048184follistatin binding0.0100925731730377
GO:0007267cell-cell signaling0.0142560561162987
GO:0048185activin binding0.0143944457968459
GO:0016486peptide hormone processing0.0160091274579621
GO:0007516hemocyte development0.0160091274579621
GO:0042386hemocyte differentiation0.017479382187223
GO:0051592response to calcium ion0.017479382187223
GO:0004977melanocortin receptor activity0.019232857529668
GO:0048731system development0.02114152694078
GO:0004999vasoactive intestinal polypeptide receptor activity0.026601334373413
GO:0019932second-messenger-mediated signaling0.0276871209729411
GO:0001541ovarian follicle development0.0353229218256498
GO:0007530sex determination0.0389003673633559
GO:0007595lactation0.0389003673633559
GO:0051704multi-organism process0.0389003673633559
GO:0016500protein-hormone receptor activity0.0392153810759798
GO:0043627response to estrogen stimulus0.0392153810759798
GO:0007190adenylate cyclase activation0.0402575045364685
GO:0022601menstrual cycle phase0.0404270122573776
GO:0022602menstrual cycle process0.0404270122573776
GO:0046983protein dimerization activity0.0404270122573776
GO:0045762positive regulation of adenylate cyclase activity0.0404270122573776
GO:0031281positive regulation of cyclase activity0.0404270122573776
GO:0051349positive regulation of lyase activity0.0404270122573776
GO:0042562hormone binding0.0404270122573776
GO:0008585female gonad development0.0413174251168308
GO:0046545development of primary female sexual characteristics0.0430154782450233
GO:0046660female sex differentiation0.0430154782450233
GO:0042698menstrual cycle0.0481783978042076
GO:0007292female gamete generation0.0495967772577401
GO:0010038response to metal ion0.0495967772577401



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><br>

Uber Anatomy
Ontology termp-valuen
pituitary gland3.29e-1952
gland of diencephalon1.55e-984
neuroendocrine gland1.55e-984
diencephalon4.76e-577
future diencephalon4.76e-577
endocrine gland1.42e-1235
regional part of forebrain1.07e-1041
forebrain1.07e-1041
anterior neural tube1.07e-1041
future forebrain1.07e-1041
endocrine system4.55e-1045
regional part of nervous system1.34e-0853
regional part of brain1.34e-0853
neural tube3.28e-0856
neural rod3.28e-0856
future spinal cord3.28e-0856
neural keel3.28e-0856
gland5.66e-0859
pre-chordal neural plate1.20e-0761
brain6.59e-0768
future brain6.59e-0768


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)
MA0003.11.22249e-07
MA0004.10.258678
MA0006.10.127228
MA0007.10.122597
MA0009.10.974804
MA0014.11.05304e-08
MA0017.10.619526
MA0019.10.0421399
MA0024.10.0451994
MA0025.10.4335
MA0027.11.39806
MA0028.10.00237158
MA0029.10.740911
MA0030.10.402604
MA0031.10.127261
MA0038.10.181784
MA0040.10.431833
MA0041.10.466281
MA0042.10.230679
MA0043.10.0800788
MA0046.10.26244
MA0048.10.834657
MA0050.10.232473
MA0051.10.0796943
MA0052.10.438484
MA0055.16.1232
MA0056.10
MA0057.10.0813124
MA0058.10.171046
MA0059.10.560635
MA0060.10.011294
MA0061.10.0364308
MA0063.10
MA0066.10.182363
MA0067.10.249504
MA0068.10.176467
MA0069.10.258385
MA0070.10.0702856
MA0071.10.873712
MA0072.10.888954
MA0073.10.0449156
MA0074.10.0791662
MA0076.10.00198607
MA0077.10.867625
MA0078.10.168469
MA0081.10.0957584
MA0083.10.282188
MA0084.10.384661
MA0087.10.882168
MA0088.10.000977818
MA0089.10
MA0090.10.940439
MA0091.14.30232
MA0092.10.308568
MA0093.10.132707
MA0095.10
MA0098.10
MA0100.10.0314397
MA0101.10.326014
MA0103.10.883413
MA0105.10.00184735
MA0106.10.00779354
MA0107.10.118639
MA0108.21.69308
MA0109.10
MA0111.10.0855886
MA0113.10.130629
MA0114.10.168451
MA0115.11.73094
MA0116.10.0767083
MA0117.10.0951982
MA0119.10.139585
MA0122.10.10652
MA0124.10.176386
MA0125.10.131237
MA0130.10
MA0131.10.0157595
MA0132.10
MA0133.10
MA0135.12.79263
MA0136.10.548378
MA0139.10.159018
MA0140.10.0561548
MA0141.10.165287
MA0142.10.257034
MA0143.10.269374
MA0144.10.647201
MA0145.10.00221987
MA0146.11.05505e-06
MA0147.10.0817954
MA0148.11.91706
MA0149.10.0154146
MA0062.23.31939e-05
MA0035.20.129625
MA0039.21.06444e-07
MA0138.20.169805
MA0002.20.195358
MA0137.20.265784
MA0104.20.0704467
MA0047.21.97851
MA0112.20.00496636
MA0065.20.0751904
MA0150.10.344369
MA0151.10
MA0152.10.0599421
MA0153.10.122947
MA0154.10.046133
MA0155.10.815797
MA0156.10.0258084
MA0157.10.0198457
MA0158.10
MA0159.10.294742
MA0160.10.765441
MA0161.10
MA0162.13.3284e-05
MA0163.10.000879552
MA0164.10.757991
MA0080.20.00627249
MA0018.20.663246
MA0099.20.00310208
MA0079.21.01254e-14
MA0102.20.413769
MA0258.10.00381001
MA0259.10.152412
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

No analysis results for this cluster

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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