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Coexpression cluster:C130

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Full id: C130_iPS_HES3GFP_H9_teratocarcinoma_testicular_colon_Alveolar



Phase1 CAGE Peaks

  Short description
Hg19::chr10:118084968..118084984,+ p@chr10:118084968..118084984
+
Hg19::chr10:118085003..118085010,+ p@chr10:118085003..118085010
+
Hg19::chr10:13390590..13390601,- p13@SEPHS1
Hg19::chr10:53798976..53798977,- p@chr10:53798976..53798977
-
Hg19::chr10:61899712..61899723,+ p@chr10:61899712..61899723
+
Hg19::chr10:6830164..6830166,- p@chr10:6830164..6830166
-
Hg19::chr10:74804784..74804793,- p@chr10:74804784..74804793
-
Hg19::chr10:92567391..92567407,+ p@chr10:92567391..92567407
+
Hg19::chr11:131123319..131123338,+ p1@ENST00000416553
Hg19::chr11:64016117..64016151,- p@chr11:64016117..64016151
-
Hg19::chr11:64016224..64016227,- p@chr11:64016224..64016227
-
Hg19::chr11:94383510..94383526,+ p@chr11:94383510..94383526
+
Hg19::chr11:94383593..94383614,+ p@chr11:94383593..94383614
+
Hg19::chr12:11762229..11762247,+ p@chr12:11762229..11762247
+
Hg19::chr12:132280681..132280688,+ p3@SFSWAP
Hg19::chr12:23738971..23738975,+ p@chr12:23738971..23738975
+
Hg19::chr12:6646472..6646496,+ p18@GAPDH
Hg19::chr12:7942020..7942031,+ p2@NANOG
Hg19::chr12:89346452..89346459,+ p@chr12:89346452..89346459
+
Hg19::chr12:9067123..9067159,+ p4@PHC1
Hg19::chr12:9067338..9067352,+ p9@PHC1
Hg19::chr13:41495638..41495642,+ p@chr13:41495638..41495642
+
Hg19::chr13:43438216..43438239,- p@chr13:43438216..43438239
-
Hg19::chr13:51743748..51743762,+ p@chr13:51743748..51743762
+
Hg19::chr13:51745257..51745261,+ p@chr13:51745257..51745261
+
Hg19::chr14:105634536..105634543,+ p@chr14:105634536..105634543
+
Hg19::chr14:21776910..21776928,- -
p@chr14:21776910..21776928
Hg19::chr14:38660185..38660188,+ p1@ENST00000555655
Hg19::chr14:84428225..84428229,+ p@chr14:84428225..84428229
+
Hg19::chr15:100980707..100980708,+ p@chr15:100980707..100980708
+
Hg19::chr15:25219499..25219545,+ p7@SNRPN
Hg19::chr15:25223016..25223033,+ p@chr15:25223016..25223033
+
Hg19::chr15:40731985..40732002,+ p17@BAHD1
Hg19::chr15:41907429..41907432,+ p1@ENST00000478625
Hg19::chr15:56363634..56363673,+ p@chr15:56363634..56363673
+
Hg19::chr15:56363776..56363799,+ p@chr15:56363776..56363799
+
Hg19::chr15:56364190..56364209,+ p@chr15:56364190..56364209
+
Hg19::chr15:56364413..56364448,+ p@chr15:56364413..56364448
+
Hg19::chr15:56364458..56364485,+ p@chr15:56364458..56364485
+
Hg19::chr15:56365001..56365013,+ +
p@chr15:56365001..56365013
Hg19::chr15:56365091..56365112,+ p@chr15:56365091..56365112
+
Hg19::chr15:56365189..56365204,+ p@chr15:56365189..56365204
+
Hg19::chr15:56365882..56365895,+ p@chr15:56365882..56365895
+
Hg19::chr15:78635894..78635913,+ p@chr15:78635894..78635913
+
Hg19::chr16:29720498..29720506,+ p@chr16:29720498..29720506
+
Hg19::chr16:29720511..29720528,+ p@chr16:29720511..29720528
+
Hg19::chr16:29740207..29740210,+ p@chr16:29740207..29740210
+
Hg19::chr16:3064994..3065011,- p@chr16:3064994..3065011
-
Hg19::chr16:3065277..3065296,- p@chr16:3065277..3065296
-
Hg19::chr16:30876603..30876606,+ p@chr16:30876603..30876606
+
Hg19::chr16:69139543..69139585,+ p2@HAS3
Hg19::chr16:9761290..9761294,- p@chr16:9761290..9761294
-
Hg19::chr16:9768264..9768287,+ p@chr16:9768264..9768287
+
Hg19::chr17:80030062..80030069,+ +
p@chr17:80030062..80030069
Hg19::chr19:3028439..3028443,- p@chr19:3028439..3028443
-
Hg19::chr19:33542309..33542310,+ p1@ENST00000463585
Hg19::chr19:54335755..54335775,+ p@chr19:54335755..54335775
+
Hg19::chr1:114574998..114575000,+ p@chr1:114574998..114575000
+
Hg19::chr1:155561105..155561109,- p1@ENST00000427475
Hg19::chr1:18624811..18624839,- p@chr1:18624811..18624839
-
Hg19::chr1:200343233..200343245,- p3@C1orf98
Hg19::chr1:200380793..200380807,+ p2@uc010ppi.1
Hg19::chr1:223202511..223202515,- p@chr1:223202511..223202515
-
Hg19::chr1:226076843..226076847,- p2@LEFTY1
Hg19::chr1:232254205..232254216,+ p@chr1:232254205..232254216
+
Hg19::chr1:46073030..46073040,- p@chr1:46073030..46073040
-
Hg19::chr1:46073987..46074014,- p@chr1:46073987..46074014
-
Hg19::chr1:55505132..55505142,+ p3@PCSK9
Hg19::chr1:63787595..63787617,- p3@ENST00000426393
Hg19::chr20:12735430..12735434,+ p@chr20:12735430..12735434
+
Hg19::chr20:12738186..12738216,+ p@chr20:12738186..12738216
+
Hg19::chr20:31372591..31372603,+ p@chr20:31372591..31372603
+
Hg19::chr20:31374351..31374362,+ p@chr20:31374351..31374362
+
Hg19::chr20:31380524..31380554,+ p@chr20:31380524..31380554
+
Hg19::chr20:31396411..31396416,+ p15@DNMT3B
Hg19::chr20:50399087..50399088,- p@chr20:50399087..50399088
-
Hg19::chr2:188430524..188430535,- p20@TFPI
Hg19::chr2:193404441..193404444,+ p@chr2:193404441..193404444
+
Hg19::chr2:202896813..202896824,+ p@chr2:202896813..202896824
+
Hg19::chr2:210164412..210164415,+ p@chr2:210164412..210164415
+
Hg19::chr2:64479926..64479928,+ p@chr2:64479926..64479928
+
Hg19::chr2:77316400..77316420,+ p@chr2:77316400..77316420
+
Hg19::chr3:109046043..109046063,- p@chr3:109046043..109046063
-
Hg19::chr3:112140140..112140170,- p@chr3:112140140..112140170
-
Hg19::chr3:162435939..162435944,+ p@chr3:162435939..162435944
+
Hg19::chr3:176044846..176044854,- p@chr3:176044846..176044854
-
Hg19::chr3:38527183..38527189,+ p@chr3:38527183..38527189
+
Hg19::chr3:46616017..46616032,+ p2@TDGF1
Hg19::chr3:46618727..46618745,+ p3@TDGF1
Hg19::chr3:54672960..54672982,- p@chr3:54672960..54672982
-
Hg19::chr3:65939393..65939412,+ p@chr3:65939393..65939412
+
Hg19::chr4:113566800..113566805,+ p@chr4:113566800..113566805
+
Hg19::chr4:113569853..113569862,- p1@ENST00000505215
p1@ENST00000509938
Hg19::chr4:113571661..113571692,- p1@ENST00000510655
Hg19::chr4:113573659..113573683,+ p@chr4:113573659..113573683
+
Hg19::chr4:150954096..150954098,+ p@chr4:150954096..150954098
+
Hg19::chr4:155665927..155665934,+ p4@LRAT
Hg19::chr4:180090669..180090673,- p@chr4:180090669..180090673
-
Hg19::chr4:187163408..187163430,+ +
p@chr4:187163408..187163430
Hg19::chr4:187163434..187163439,+ p@chr4:187163434..187163439
+
Hg19::chr4:187171657..187171667,+ p@chr4:187171657..187171667
+
Hg19::chr4:188918405..188918406,+ p@chr4:188918405..188918406
+
Hg19::chr4:379933..379948,+ +
p@chr4:379933..379948
Hg19::chr4:57458618..57458624,+ p@chr4:57458618..57458624
+
Hg19::chr4:62635359..62635371,- p@chr4:62635359..62635371
-
Hg19::chr5:120035355..120035366,- p@chr5:120035355..120035366
-
Hg19::chr5:123833031..123833035,+ p@chr5:123833031..123833035
+
Hg19::chr5:142082957..142082972,+ p@chr5:142082957..142082972
+
Hg19::chr5:147248693..147248701,- p@chr5:147248693..147248701
-
Hg19::chr5:80501452..80501465,+ p1@RNU5D-1
p1@RNU5E-1
Hg19::chr6:121759714..121759721,+ p@chr6:121759714..121759721
+
Hg19::chr6:132224075..132224083,+ p@chr6:132224075..132224083
+
Hg19::chr6:132234089..132234094,+ p@chr6:132234089..132234094
+
Hg19::chr6:15487707..15487724,+ p@chr6:15487707..15487724
+
Hg19::chr6:18759117..18759122,- p@chr6:18759117..18759122
-
Hg19::chr6:33084446..33084462,+ p@chr6:33084446..33084462
+
Hg19::chr6:71377348..71377355,+ p10@SMAP1
Hg19::chr6:77271226..77271236,+ +
p@chr6:77271226..77271236
Hg19::chr7:121715171..121715176,- p@chr7:121715171..121715176
-
Hg19::chr7:138144581..138144590,- p@chr7:138144581..138144590
-
Hg19::chr7:51395308..51395318,+ p@chr7:51395308..51395318
+
Hg19::chr7:83090055..83090066,+ p@chr7:83090055..83090066
+
Hg19::chr7:89853761..89853768,+ p@chr7:89853761..89853768
+
Hg19::chr7:93269596..93269602,+ p@chr7:93269596..93269602
+
Hg19::chr7:99986543..99986546,+ p@chr7:99986543..99986546
+
Hg19::chr8:115308332..115308341,+ p@chr8:115308332..115308341
+
Hg19::chr8:128428066..128428078,+ p1@POU5F1B
Hg19::chr8:494169..494176,+ p@chr8:494169..494176
+
Hg19::chr8:61852178..61852208,+ p@chr8:61852178..61852208
+
Hg19::chr8:72587586..72587591,+ p1@ENST00000521131
Hg19::chr8:73958509..73958513,+ p@chr8:73958509..73958513
+
Hg19::chr9:12948720..12948724,+ p@chr9:12948720..12948724
+
Hg19::chr9:76707423..76707428,+ p@chr9:76707423..76707428
+
Hg19::chrX:16141667..16141707,+ p1@GRPR
Hg19::chrX:2719421..2719424,- p@chrX:2719421..2719424
-
Hg19::chrX:70288369..70288404,- p3@SNX12
Hg19::chrX:83004216..83004220,- p@chrX:83004216..83004220
-
Hg19::chrX:91359700..91359713,- p1@ENST00000540909
p1@uc004efp.1
Hg19::chrX:91359754..91359757,- p2@ENST00000540909
p2@uc004efp.1


Enriched pathways on this co-expression cluster
Summary:


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.
Analyst: Emmanuel Dimont

link to source dataset


data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster
Summary: 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.
Analyst: Erik Arner



link to source dataset


data

GO IDGO nameFDR corrected p-value
GO:0032870cellular response to hormone stimulus0.0466266336983398
GO:0032869cellular response to insulin stimulus0.0466266336983398
GO:0047173phosphatidylcholine-retinol O-acyltransferase activity0.0466266336983398
GO:0008326site-specific DNA-methyltransferase (cytosine-specific) activity0.0466266336983398



Enriched sample ontology terms on this co-expression cluster
Summary: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. Analyst: Hideya Kawaji



links to source dataset

cell_data
uberon_data

disease_data

Cell Type
Ontology termp-valuen
embryonic stem cell1.01e-705
neuron1.97e-226
neuroblast1.97e-226
electrically signaling cell1.97e-226
germ line cell1.48e-187
germ cell1.48e-187
neuronal stem cell5.37e-178
melanocyte1.90e-1310
melanoblast1.90e-1310
pigment cell8.96e-1014
neurectodermal cell3.17e-0859
neurecto-epithelial cell5.34e-0720
Uber Anatomy
Ontology termp-valuen
testis2.53e-168
male reproductive organ4.77e-1211
gonad6.34e-1121
indifferent external genitalia6.34e-1121
indifferent gonad6.34e-1121
gonad primordium6.34e-1121
external genitalia1.93e-1022
Disease
Ontology termp-valuen
germ cell and embryonal cancer7.62e-1622
germ cell cancer7.62e-1622


Overrepresented TFBS (DNA) motifs on this co-expression cluster
Summary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs

data

Novel motifs


JASPAR motifs
Motifs-log10(p-value)
MA0003.15.73775e-15
MA0004.10.00206588
MA0006.10.116725
MA0007.11.50463
MA0009.10.184881
MA0014.12.33723e-09
MA0017.10.0421896
MA0019.10.625415
MA0024.10.105081
MA0025.10.0966747
MA0027.11.30259
MA0028.10.00475625
MA0029.10.523768
MA0030.10.110209
MA0031.10.072248
MA0038.10.0897108
MA0040.11.67096
MA0041.10.24706
MA0042.13.75009
MA0043.10.185158
MA0046.10.395528
MA0048.18.91147e-05
MA0050.10.289724
MA0051.10.665293
MA0052.10.545567
MA0055.10.00163221
MA0056.10
MA0057.10.353198
MA0058.10.000238717
MA0059.10.00127211
MA0060.13.6508e-05
MA0061.10.156604
MA0063.10
MA0066.10.178825
MA0067.10.190212
MA0068.10.0541249
MA0069.10.389286
MA0070.11.02947
MA0071.10.985343
MA0072.10.364342
MA0073.14.61825e-10
MA0074.11.18292
MA0076.10.0186176
MA0077.10.152998
MA0078.10.196031
MA0081.10.0628421
MA0083.10.0514565
MA0084.10.313207
MA0087.11.00599
MA0088.17.48404e-05
MA0089.10
MA0090.11.3693
MA0091.11.39469
MA0092.10.496173
MA0093.13.59406e-05
MA0095.10
MA0098.10
MA0100.10.102245
MA0101.10.0223386
MA0103.12.04881
MA0105.10.0295282
MA0106.10.129979
MA0107.10.0529835
MA0108.25.56344
MA0109.10
MA0111.10.299005
MA0113.10.14853
MA0114.10.119371
MA0115.10.147682
MA0116.10.0330304
MA0117.10.0607969
MA0119.10.146634
MA0122.10.0695762
MA0124.10.795162
MA0125.10.299757
MA0130.10
MA0131.10.104303
MA0132.10
MA0133.10
MA0135.10.212475
MA0136.10.095958
MA0139.10.00288699
MA0140.17.80874
MA0141.10.10875
MA0142.110.2407
MA0143.15.47023
MA0144.10.263435
MA0145.10.0588186
MA0146.10.000130642
MA0147.12.17774e-05
MA0148.10.399497
MA0149.10.488476
MA0062.20.000269651
MA0035.210.3622
MA0039.20.00676531
MA0138.20.0307043
MA0002.20.0168923
MA0137.20.346194
MA0104.27.29851e-06
MA0047.20.569495
MA0112.20.00863397
MA0065.20.153202
MA0150.10.0477956
MA0151.10
MA0152.10.75958
MA0153.10.281374
MA0154.10.00637974
MA0155.10.0207986
MA0156.10.00588225
MA0157.10.263384
MA0158.10
MA0159.11.15077
MA0160.10.635171
MA0161.10
MA0162.11.78135e-10
MA0163.13.81439e-06
MA0164.11.3109
MA0080.20.00916313
MA0018.20.131488
MA0099.20.024065
MA0079.28.09627e-07
MA0102.20.340338
MA0258.10.300573
MA0259.10.116201
MA0442.10


ENCODE TF ChIP-seq peak enrichment analysis
Summary: 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.
Analyst: Erik Arner



link to source dataset


data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NANOG#79923245.049458154994997.33000878949244e-118.06679439373868e-09
POU5F1#54601024.13231665121621.93039694695569e-112.32000836298164e-09
TAF7#6879252.056307446928760.0004233126616163930.00395972692042584



Relative expression of the co-expression cluster
Summary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data