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

Latest revision as of 10:35, 17 September 2013


Full id: C115_pituitary_Neural_caudate_putamen_amygdala_medulla_hippocampus



Phase1 CAGE Peaks

Hg19::chr10:106423509..106423521,+p@chr10:106423509..106423521
+
Hg19::chr10:123959529..123959547,+p@chr10:123959529..123959547
+
Hg19::chr10:18579999..18580012,-p@chr10:18579999..18580012
-
Hg19::chr10:18580030..18580043,-p@chr10:18580030..18580043
-
Hg19::chr10:18580125..18580134,+p@chr10:18580125..18580134
+
Hg19::chr10:18580138..18580153,+p@chr10:18580138..18580153
+
Hg19::chr11:111601666..111601697,-p@chr11:111601666..111601697
-
Hg19::chr11:68419276..68419303,-p@chr11:68419276..68419303
-
Hg19::chr11:9088284..9088330,-p4@SCUBE2
Hg19::chr12:113697781..113697814,+p7@TPCN1
Hg19::chr12:80603044..80603046,+p1@OTOGL
Hg19::chr12:89881337..89881342,-p@chr12:89881337..89881342
-
Hg19::chr12:89881348..89881356,-p@chr12:89881348..89881356
-
Hg19::chr13:40924577..40924587,-p2@ENST00000400432
Hg19::chr13:40924605..40924623,-p1@ENST00000400432
Hg19::chr13:51617751..51617754,+p@chr13:51617751..51617754
+
Hg19::chr14:62584108..62584133,+p1@FLJ43390
Hg19::chr14:62584173..62584178,+p2@ENST00000334389
Hg19::chr15:24157554..24157578,+p@chr15:24157554..24157578
+
Hg19::chr15:33445488..33445523,-p@chr15:33445488..33445523
-
Hg19::chr15:33445536..33445552,-p@chr15:33445536..33445552
-
Hg19::chr15:48681810..48681835,-p@chr15:48681810..48681835
-
Hg19::chr15:62352961..62352973,-p8@VPS13C
Hg19::chr15:89147906..89147920,+p@chr15:89147906..89147920
+
Hg19::chr16:21049173..21049231,-p@chr16:21049173..21049231
-
Hg19::chr17:18021982..18021985,+p3@MYO15A
Hg19::chr17:191188..191219,-p@chr17:191188..191219
-
Hg19::chr17:191225..191238,-p@chr17:191225..191238
-
Hg19::chr17:61995906..61995914,-p6@AB591020
Hg19::chr17:61995979..61995990,-p2@AB591020
Hg19::chr17:61995995..61996002,-p3@AB591020
Hg19::chr17:61996018..61996019,-p5@AB591020
Hg19::chr17:61996155..61996158,-p5@GH1
Hg19::chr17:61996160..61996176,-p3@GH1
Hg19::chr17:61996252..61996253,-p2@GH1
p3@CSHL1
Hg19::chr17:61996393..61996421,-p4@CSHL1
p4@GH1
Hg19::chr18:21824830..21824832,-p@chr18:21824830..21824832
-
Hg19::chr19:14095105..14095108,-p@chr19:14095105..14095108
-
Hg19::chr19:14946017..14946050,-p3@OR7A5
Hg19::chr19:2608406..2608413,-p@chr19:2608406..2608413
-
Hg19::chr19:46801484..46801498,+p9@HIF3A
Hg19::chr19:4770772..4770775,+p1@MIR7-3
Hg19::chr19:47793168..47793181,+p@chr19:47793168..47793181
+
Hg19::chr1:109656644..109656670,+p4@KIAA1324
Hg19::chr1:114483276..114483289,+p@chr1:114483276..114483289
+
Hg19::chr1:159116850..159116858,-p10@AIM2
Hg19::chr1:159116897..159116903,-p12@AIM2
Hg19::chr1:168250110..168250120,+p2@TBX19
Hg19::chr1:168250194..168250197,+p3@TBX19
Hg19::chr1:206942410..206942414,-p@chr1:206942410..206942414
-
Hg19::chr1:240286421..240286436,+p@chr1:240286421..240286436
+
Hg19::chr1:43400328..43400332,+p@chr1:43400328..43400332
+
Hg19::chr1:7709325..7709329,+p@chr1:7709325..7709329
+
Hg19::chr20:20505922..20505946,-p@chr20:20505922..20505946
-
Hg19::chr20:31667446..31667451,+p1@BPIFB4
Hg19::chr20:33451327..33451358,-p4@GGT7
Hg19::chr20:57415768..57415803,+p@chr20:57415768..57415803
+
Hg19::chr20:58401707..58401714,+p@chr20:58401707..58401714
+
Hg19::chr20:58401898..58401905,+p@chr20:58401898..58401905
+
Hg19::chr22:45015998..45016005,-p@chr22:45015998..45016005
-
Hg19::chr2:130941446..130941486,-p1@CU676019
Hg19::chr2:1714065..1714071,+p@chr2:1714065..1714071
+
Hg19::chr2:187287127..187287143,-p@chr2:187287127..187287143
-
Hg19::chr2:211830430..211830435,+p@chr2:211830430..211830435
+
Hg19::chr2:211830446..211830457,+p@chr2:211830446..211830457
+
Hg19::chr2:241080084..241080093,-p5@OTOS
Hg19::chr2:25383828..25383855,-p4@POMC
Hg19::chr2:25383910..25383918,-p17@POMC
Hg19::chr2:25383947..25383959,+p@chr2:25383947..25383959
+
Hg19::chr2:25391399..25391417,-p8@POMC
Hg19::chr2:25391425..25391439,-p10@POMC
Hg19::chr2:25391442..25391456,-p1@POMC
Hg19::chr2:25391468..25391485,-p5@POMC
Hg19::chr2:25391507..25391519,-p9@POMC
Hg19::chr2:25391657..25391666,-p14@POMC
Hg19::chr2:25391815..25391821,-p13@POMC
Hg19::chr2:45161466..45161475,+p@chr2:45161466..45161475
+
Hg19::chr2:58113353..58113375,-p@chr2:58113353..58113375
-
Hg19::chr2:58113386..58113399,-p@chr2:58113386..58113399
-
Hg19::chr2:58113402..58113415,-p@chr2:58113402..58113415
-
Hg19::chr2:58113422..58113431,-p@chr2:58113422..58113431
-
Hg19::chr2:70312872..70312889,-p23@PCBP1-AS1
Hg19::chr2:70312899..70312908,-p44@PCBP1-AS1
Hg19::chr2:7497646..7497649,+p@chr2:7497646..7497649
+
Hg19::chr2:98962912..98962924,+p2@CNGA3
Hg19::chr3:108321623..108321685,+p4@DZIP3
Hg19::chr3:114477881..114477914,-p17@ZBTB20
Hg19::chr3:118521917..118521922,-p@chr3:118521917..118521922
-
Hg19::chr3:130248877..130248886,+p@chr3:130248877..130248886
+
Hg19::chr3:130248915..130248922,+p@chr3:130248915..130248922
+
Hg19::chr3:130248948..130248959,+p@chr3:130248948..130248959
+
Hg19::chr3:133115455..133115457,+p@chr3:133115455..133115457
+
Hg19::chr3:154042775..154042780,-p8@DHX36
Hg19::chr3:185324217..185324224,+p1@ENST00000455173
Hg19::chr3:24206603..24206613,-p17@THRB
Hg19::chr3:24206934..24206942,-p24@THRB
Hg19::chr3:4774755..4774765,+p@chr3:4774755..4774765
+
Hg19::chr3:58572679..58572682,-p30@FAM107A
Hg19::chr3:58572689..58572703,-p6@FAM107A
Hg19::chr3:58572720..58572733,-p11@FAM107A
Hg19::chr3:58572734..58572746,-p8@FAM107A
Hg19::chr3:58572760..58572774,-p9@FAM107A
Hg19::chr3:79817089..79817094,-p27@ROBO1
Hg19::chr3:87325636..87325643,-p2@POU1F1
Hg19::chr3:87325728..87325739,-p1@POU1F1
Hg19::chr4:108815402..108815408,+p13@SGMS2
Hg19::chr4:1352813..1352818,-p@chr4:1352813..1352818
-
Hg19::chr4:6635531..6635534,+p@chr4:6635531..6635534
+
Hg19::chr4:70518941..70518967,-p1@UGT2A1
p1@UGT2A2
Hg19::chr4:76359403..76359419,-p1@ENST00000510744
Hg19::chr4:8103287..8103292,+p@chr4:8103287..8103292
+
Hg19::chr5:132668491..132668494,+p@chr5:132668491..132668494
+
Hg19::chr5:134509776..134509792,+p@chr5:134509776..134509792
+
Hg19::chr5:134509799..134509814,+p@chr5:134509799..134509814
+
Hg19::chr5:158737729..158737738,-p@chr5:158737729..158737738
-
Hg19::chr5:158737824..158737862,+p1@ENST00000521472
Hg19::chr5:165553564..165553568,-p@chr5:165553564..165553568
-
Hg19::chr5:77409743..77409752,-p6@AP3B1
Hg19::chr6:12717892..12717903,+p23@PHACTR1
Hg19::chr6:139155017..139155049,-p@chr6:139155017..139155049
-
Hg19::chr6:163149056..163149101,+p2@PACRG
Hg19::chr6:168333280..168333294,+p9@MLLT4
Hg19::chr6:22287516..22287522,-p@chr6:22287516..22287522
-
Hg19::chr6:22287527..22287538,-p@chr6:22287527..22287538
-
Hg19::chr6:22287619..22287636,-p@chr6:22287619..22287636
-
Hg19::chr6:22287669..22287676,-p@chr6:22287669..22287676
-
Hg19::chr6:22287695..22287700,-p@chr6:22287695..22287700
-
Hg19::chr6:22297257..22297272,-p1@PRL
Hg19::chr6:82727317..82727327,+p@chr6:82727317..82727327
+
Hg19::chr6:88805080..88805083,-p@chr6:88805080..88805083
-
Hg19::chr7:103549700..103549706,-p@chr7:103549700..103549706
-
Hg19::chr7:150644605..150644616,-p@chr7:150644605..150644616
-
Hg19::chr7:31003560..31003576,+p5@GHRHR
Hg19::chr7:31003580..31003589,+p6@GHRHR
Hg19::chr7:31006649..31006651,+p@chr7:31006649..31006651
+
Hg19::chr7:31009189..31009197,+p11@GHRHR
Hg19::chr7:31010569..31010576,+p9@GHRHR
Hg19::chr7:31010582..31010601,+p4@GHRHR
Hg19::chr7:31016265..31016282,+p@chr7:31016265..31016282
+
Hg19::chr7:95114742..95114776,+p4@ASB4
Hg19::chr8:1066886..1066919,+p@chr8:1066886..1066919
+
Hg19::chr8:107844170..107844179,+p@chr8:107844170..107844179
+
Hg19::chr8:130017368..130017390,+p@chr8:130017368..130017390
+
Hg19::chr9:135964996..135965001,+p@chr9:135964996..135965001
+
Hg19::chr9:135965121..135965124,+p@chr9:135965121..135965124
+
Hg19::chr9:547212..547233,+p28@KANK1
Hg19::chr9:75568126..75568136,-p13@ALDH1A1
Hg19::chr9:75568163..75568197,-p8@ALDH1A1
Hg19::chrX:111923145..111923173,-p1@LHFPL1
Hg19::chrX:130215591..130215605,+p@chrX:130215591..130215605
+
Hg19::chrX:130215610..130215625,+p@chrX:130215610..130215625
+
Hg19::chrX:130215640..130215656,+p@chrX:130215640..130215656
+
Hg19::chrX:130423240..130423288,-p1@IGSF1
Hg19::chrX:130423386..130423397,-p6@IGSF1
Hg19::chrX:147887590..147887594,+p@chrX:147887590..147887594
+
Hg19::chrX:150345054..150345060,+p1@GPR50
Hg19::chrX:24169518..24169522,+p8@ZFX
Hg19::chrX:38147077..38147085,-p@chrX:38147077..38147085
-
Hg19::chrX:38183144..38183165,-p@chrX:38183144..38183165
-
Hg19::chrX:9528518..9528536,+p@chrX:9528518..9528536
+


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
2.57139298499459e-050.01627691759501575272Neuroactive ligand-receptor interaction (KEGG):04080



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:0050954sensory perception of mechanical stimulus0.0393796071001252
GO:0007605sensory perception of sound0.0393796071001252
GO:0005515protein binding0.0393796071001252
GO:0032501multicellular organismal process0.0445827919264483
GO:0048187inhibin beta-B binding0.0445827919264483
GO:0031593polyubiquitin binding0.0445827919264483
GO:0005179hormone activity0.0445827919264483
GO:0007600sensory perception0.0445827919264483
GO:0051138positive regulation of NK T cell differentiation0.0445827919264483
GO:0033188sphingomyelin synthase activity0.0445827919264483
GO:0047493ceramide cholinephosphotransferase activity0.0445827919264483
GO:0048007antigen processing and presentation, exogenous lipid antigen via MHC class Ib0.0445827919264483
GO:0001865NK T cell differentiation0.0445827919264483
GO:0051136regulation of NK T cell differentiation0.0445827919264483
GO:0048186inhibin beta-A binding0.0445827919264483
GO:0005148prolactin receptor binding0.0445827919264483
GO:0048856anatomical structure development0.0445827919264483
GO:0003008system process0.0445827919264483
GO:0002475antigen processing and presentation via MHC class Ib0.0445827919264483
GO:0021984adenohypophysis development0.0445827919264483
GO:0001758retinal dehydrogenase activity0.0445827919264483
GO:0008046axon guidance receptor activity0.0445827919264483
GO:0006686sphingomyelin biosynthetic process0.0445827919264483
GO:0048003antigen processing and presentation of lipid antigen via MHC class Ib0.0445827919264483
GO:0003712transcription cofactor activity0.0445827919264483



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)
MA0003.16.56662e-07
MA0004.10.0658703
MA0006.10.0526196
MA0007.110.2839
MA0009.10.926808
MA0014.10.000231996
MA0017.11.57643
MA0019.11.48048
MA0024.10.0727794
MA0025.10.929151
MA0027.11.24314
MA0028.10.00406943
MA0029.10.666569
MA0030.10.634367
MA0031.10.270298
MA0038.11.179
MA0040.10.417607
MA0041.10.0408253
MA0042.10.390637
MA0043.10.590008
MA0046.10.308427
MA0048.10.0033594
MA0050.10.0554183
MA0051.10.193729
MA0052.10.425328
MA0055.10.493952
MA0056.10
MA0057.10.266424
MA0058.10.0964837
MA0059.10.00491091
MA0060.10.00318017
MA0061.14.4271e-05
MA0063.10
MA0066.12.54068
MA0067.10.156922
MA0068.10.141812
MA0069.10.555546
MA0070.10.287215
MA0071.10.524342
MA0072.10.830272
MA0073.12.00267e-12
MA0074.10.313753
MA0076.19.89943e-05
MA0077.10.270549
MA0078.10.130471
MA0081.10.0543416
MA0083.10.0363247
MA0084.10.271361
MA0087.10.822687
MA0088.10.0161323
MA0089.10
MA0090.10.0893791
MA0091.14.49857
MA0092.10.983026
MA0093.10.03126
MA0095.10
MA0098.10
MA0100.10.362682
MA0101.10.0596478
MA0103.13.05294
MA0105.11.81521e-05
MA0106.10.0320302
MA0107.10.00954083
MA0108.24.25484
MA0109.10
MA0111.10.0301857
MA0113.14.14305
MA0114.11.06113
MA0115.10.118547
MA0116.10.445386
MA0117.10.168187
MA0119.10.184847
MA0122.10.190324
MA0124.10.673857
MA0125.10.239005
MA0130.10
MA0131.10.0211279
MA0132.10
MA0133.10
MA0135.18.25193
MA0136.10.0211283
MA0139.10.522951
MA0140.10.135548
MA0141.12.12701
MA0142.11.96968
MA0143.10.317935
MA0144.10.749709
MA0145.10.000469326
MA0146.13.93146e-06
MA0147.10.00567842
MA0148.10.540725
MA0149.10.0629036
MA0062.29.78473e-05
MA0035.20.701262
MA0039.22.07494e-12
MA0138.21.48558
MA0002.20.0616754
MA0137.20.274564
MA0104.20.00307953
MA0047.21.07621
MA0112.20.0775456
MA0065.21.85206
MA0150.10.573366
MA0151.10
MA0152.10.375275
MA0153.10.222631
MA0154.10.247315
MA0155.10.0742586
MA0156.10.00180131
MA0157.10.333265
MA0158.10
MA0159.10.10068
MA0160.10.436547
MA0161.10
MA0162.18.15106e-09
MA0163.13.17275e-06
MA0164.12.42929
MA0080.20.0159024
MA0018.20.164066
MA0099.20.0118419
MA0079.29.78711e-11
MA0102.21.46311
MA0258.10.937556
MA0259.10.0281057
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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