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Coexpression cluster:C141

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Full id: C141_Hodgkin_acute_thymus_chronic_vein_CD4_B



Phase1 CAGE Peaks

  Short description
Hg19::chr10:73637839..73637853,+ p1@ENST00000441348
Hg19::chr10:73637855..73637875,+ p2@ENST00000441348
Hg19::chr10:73638582..73638591,- -
p@chr10:73638582..73638591
Hg19::chr10:92706978..92707003,+ p@chr10:92706978..92707003
+
Hg19::chr10:92707051..92707066,+ p@chr10:92707051..92707066
+
Hg19::chr11:118213455..118213462,- p4@CD3D
Hg19::chr11:118214883..118214897,+ p5@CD3G
Hg19::chr11:134594759..134594800,+ p@chr11:134594759..134594800
+
Hg19::chr12:123528254..123528260,- p@chr12:123528254..123528260
-
Hg19::chr12:133423989..133423993,- p9@CHFR
Hg19::chr12:96312497..96312514,+ p@chr12:96312497..96312514
+
Hg19::chr13:100993767..100993771,+ p@chr13:100993767..100993771
+
Hg19::chr13:105489602..105489620,- p@chr13:105489602..105489620
-
Hg19::chr13:105490171..105490180,- p@chr13:105490171..105490180
-
Hg19::chr13:105490195..105490246,- p@chr13:105490195..105490246
-
Hg19::chr13:105490252..105490261,- p@chr13:105490252..105490261
-
Hg19::chr13:105490265..105490298,- p@chr13:105490265..105490298
-
Hg19::chr13:105490330..105490339,- p@chr13:105490330..105490339
-
Hg19::chr13:105493631..105493638,- p@chr13:105493631..105493638
-
Hg19::chr13:105493668..105493673,- p@chr13:105493668..105493673
-
Hg19::chr14:22433576..22433585,+ p3@TRAV12-3
Hg19::chr14:22433621..22433634,+ p1@TRAV12-3
Hg19::chr14:22433639..22433648,+ p2@TRAV12-3
Hg19::chr14:22433668..22433669,+ p5@TRAV12-3
Hg19::chr14:22433675..22433678,+ p4@TRAV12-3
Hg19::chr14:22433688..22433700,+ p1@uc010tmk.1
Hg19::chr14:22782730..22782741,- p@chr14:22782730..22782741
-
Hg19::chr14:22782867..22782896,+ p1@uc001wdq.2
Hg19::chr15:100656334..100656337,- -
p@chr15:100656334..100656337
Hg19::chr15:100875730..100875747,- p@chr15:100875730..100875747
-
Hg19::chr15:100875760..100875766,- p@chr15:100875760..100875766
-
Hg19::chr15:100875799..100875802,- -
p@chr15:100875799..100875802
Hg19::chr15:100879294..100879309,- p4@ADAMTS17
Hg19::chr15:100879323..100879339,- p3@ADAMTS17
Hg19::chr15:23749153..23749162,+ p@chr15:23749153..23749162
+
Hg19::chr15:23749170..23749178,+ p@chr15:23749170..23749178
+
Hg19::chr15:58702742..58702777,+ p1@LIPC
Hg19::chr15:93774987..93775010,+ p@chr15:93774987..93775010
+
Hg19::chr15:99816268..99816283,+ p@chr15:99816268..99816283
+
Hg19::chr16:70729549..70729555,- p9@VAC14
Hg19::chr17:54889185..54889192,- p@chr17:54889185..54889192
-
Hg19::chr17:66177017..66177028,+ p@chr17:66177017..66177028
+
Hg19::chr17:78695021..78695044,+ p1@BC127818
Hg19::chr18:13612668..13612678,+ p@chr18:13612668..13612678
+
Hg19::chr18:66382562..66382574,+ p5@CCDC102B
Hg19::chr18:76438418..76438431,- p@chr18:76438418..76438431
-
Hg19::chr1:151798753..151798775,+ p@chr1:151798753..151798775
+
Hg19::chr1:158218146..158218178,+ p@chr1:158218146..158218178
+
Hg19::chr1:158223689..158223707,+ p15@CD1A
Hg19::chr1:158301588..158301605,- p17@CD1B
Hg19::chr1:199147944..199147956,- p@chr1:199147944..199147956
-
Hg19::chr1:199147989..199147994,- p@chr1:199147989..199147994
-
Hg19::chr1:199253025..199253034,- p@chr1:199253025..199253034
-
Hg19::chr1:199253117..199253122,- p@chr1:199253117..199253122
-
Hg19::chr1:31971796..31971801,+ p1@uc001bsx.2
p2@uc001bsw.1
Hg19::chr1:31971816..31971824,+ p1@uc001bsw.1
Hg19::chr1:31971828..31971840,+ p1@LOC149086
Hg19::chr1:31978612..31978615,+ p@chr1:31978612..31978615
+
Hg19::chr1:31993101..31993106,+ +
p@chr1:31993101..31993106
Hg19::chr1:31999815..31999818,+ p@chr1:31999815..31999818
+
Hg19::chr20:30272415..30272424,- p@chr20:30272415..30272424
-
Hg19::chr20:43251533..43251545,- p@chr20:43251533..43251545
-
Hg19::chr20:61638313..61638318,- p1@BHLHE23
Hg19::chr20:61638491..61638530,+ p@chr20:61638491..61638530
+
Hg19::chr20:61639423..61639436,+ p@chr20:61639423..61639436
+
Hg19::chr20:61644926..61644929,+ p@chr20:61644926..61644929
+
Hg19::chr21:47052212..47052255,+ p@chr21:47052212..47052255
+
Hg19::chr22:20088313..20088348,+ p@chr22:20088313..20088348
+
Hg19::chr22:24823536..24823551,- p@chr22:24823536..24823551
-
Hg19::chr22:41080903..41080912,- p@chr22:41080903..41080912
-
Hg19::chr22:41080919..41080941,- p@chr22:41080919..41080941
-
Hg19::chr2:128399735..128399738,- p54@LIMS2
Hg19::chr2:128399756..128399791,- p12@LIMS2
Hg19::chr2:128399812..128399825,- p31@LIMS2
Hg19::chr2:132162757..132162798,+ p@chr2:132162757..132162798
+
Hg19::chr2:147655803..147655815,- p@chr2:147655803..147655815
-
Hg19::chr2:156002395..156002400,- p@chr2:156002395..156002400
-
Hg19::chr2:40146823..40146848,+ p1@ENST00000418854
Hg19::chr3:109282218..109282225,+ p@chr3:109282218..109282225
+
Hg19::chr3:140950191..140950210,+ p2@ACPL2
Hg19::chr3:141685754..141685759,- p@chr3:141685754..141685759
-
Hg19::chr3:141868293..141868355,- p2@TFDP2
Hg19::chr3:45920084..45920088,- -
p@chr3:45920084..45920088
Hg19::chr3:45957190..45957235,- p2@LZTFL1
Hg19::chr3:69435554..69435561,- p41@FRMD4B
Hg19::chr4:169433194..169433201,+ p48@PALLD
Hg19::chr4:8231045..8231053,+ p@chr4:8231045..8231053
+
Hg19::chr4:8231096..8231103,+ p@chr4:8231096..8231103
+
Hg19::chr5:150591651..150591662,+ p13@GM2A
Hg19::chr5:150591663..150591668,+ p20@GM2A
Hg19::chr5:150591678..150591733,+ p7@GM2A
Hg19::chr5:150591738..150591749,+ p14@GM2A
Hg19::chr5:150592248..150592272,+ p@chr5:150592248..150592272
+
Hg19::chr5:150592285..150592315,+ +
p@chr5:150592285..150592315
Hg19::chr5:150595990..150595994,+ p@chr5:150595990..150595994
+
Hg19::chr5:61434588..61434602,- p@chr5:61434588..61434602
-
Hg19::chr6:150312342..150312382,- p@chr6:150312342..150312382
-
Hg19::chr6:25094713..25094717,- p@chr6:25094713..25094717
-
Hg19::chr6:25167681..25167698,- p@chr6:25167681..25167698
-
Hg19::chr6:25167706..25167719,- p@chr6:25167706..25167719
-
Hg19::chr6:41978449..41978456,+ p@chr6:41978449..41978456
+
Hg19::chr7:133168808..133168816,- p@chr7:133168808..133168816
-
Hg19::chr7:133168901..133168912,- p@chr7:133168901..133168912
-
Hg19::chr7:133168986..133168997,- p@chr7:133168986..133168997
-
Hg19::chr7:133169045..133169060,- p@chr7:133169045..133169060
-
Hg19::chr7:142045038..142045063,+ p2@TRBV4-2
Hg19::chr7:142045246..142045258,+ p1@TRBV4-2
Hg19::chr7:142045295..142045317,+ p1@uc003vxp.3
Hg19::chr7:142045601..142045622,+ p1@S82067
Hg19::chr7:142494672..142494705,+ p1@TRBJ2-4
Hg19::chr7:38403077..38403086,- p1@TRGV2
Hg19::chr7:49618973..49619001,+ p@chr7:49618973..49619001
+
Hg19::chr7:49619037..49619042,+ p@chr7:49619037..49619042
+
Hg19::chr8:124084747..124084757,+ p6@WDR67
Hg19::chr8:130253461..130253480,- p2@LOC728724
Hg19::chr8:130253482..130253510,- p1@LOC728724
Hg19::chr8:130253513..130253524,- p1@ENST00000509893
p1@uc003ysp.1
p1@uc010mdr.1
Hg19::chr8:130427796..130427799,+ p3@ENST00000519048
Hg19::chr8:134072500..134072514,- p6@SLA
Hg19::chr8:2162920..2162931,+ p@chr8:2162920..2162931
+
Hg19::chr8:61969632..61969641,+ p8@CLVS1
Hg19::chr9:112179928..112179940,- p9@PTPN3
Hg19::chr9:112179990..112179998,- p17@PTPN3
Hg19::chr9:136568685..136568722,- p4@SARDH


Enriched pathways on this co-expression clusterSummary:
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


p.valueFDRnGenesnPathwayName
1.63118747922973e-060.00103254167435242488Hematopoietic cell lineage (KEGG):04640
8.45420275641347e-060.002675755172404864133T Cell Receptor Signaling Pathway (Wikipathways):WP69



Enriched Gene Ontology terms on this co-expression clusterSummary: 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:0042101T cell receptor complex0.00668629716819874
GO:0001772immunological synapse0.00687743094890173
GO:0044242cellular lipid catabolic process0.023972953605579
GO:0030290sphingolipid activator protein activity0.023972953605579
GO:0032428beta-N-acetylgalactosaminidase activity0.023972953605579
GO:0043395heparan sulfate proteoglycan binding0.023972953605579
GO:0043394proteoglycan binding0.023972953605579
GO:0044248cellular catabolic process0.023972953605579
GO:0005889hydrogen:potassium-exchanging ATPase complex0.023972953605579
GO:0051371muscle alpha-actinin binding0.023972953605579
GO:0043368positive T cell selection0.023972953605579
GO:0016004phospholipase activator activity0.023972953605579
GO:0046337phosphatidylethanolamine metabolic process0.023972953605579
GO:0045179apical cortex0.023972953605579
GO:0009313oligosaccharide catabolic process0.023972953605579
GO:0045059positive thymic T cell selection0.023972953605579
GO:0005319lipid transporter activity0.0244925688648456
GO:0042110T cell activation0.0244925688648456
GO:0046982protein heterodimerization activity0.0244925688648456
GO:0019898extrinsic to membrane0.0244925688648456
GO:0051393alpha-actinin binding0.0244925688648456
GO:0046461neutral lipid catabolic process0.0244925688648456
GO:0042608T cell receptor binding0.0244925688648456
GO:0043235receptor complex0.0244925688648456
GO:0009056catabolic process0.0252198311256358
GO:0008480sarcosine dehydrogenase activity0.0264389011852018
GO:0004563beta-N-acetylhexosaminidase activity0.0264389011852018
GO:0006689ganglioside catabolic process0.0264389011852018
GO:0046473phosphatidic acid metabolic process0.0264389011852018
GO:0006869lipid transport0.0290350396039018
GO:0046479glycosphingolipid catabolic process0.0290350396039018
GO:0045061thymic T cell selection0.0290350396039018
GO:0042805actinin binding0.0290350396039018
GO:0016042lipid catabolic process0.0301622994414704
GO:0001948glycoprotein binding0.0311582336324494
GO:0009898internal side of plasma membrane0.0311582336324494
GO:0046649lymphocyte activation0.0311582336324494
GO:0046470phosphatidylcholine metabolic process0.0343771378066479
GO:0019377glycolipid catabolic process0.0343771378066479
GO:0008092cytoskeletal protein binding0.0350739049383545
GO:0019915sequestering of lipid0.0350739049383545
GO:0001573ganglioside metabolic process0.0350739049383545
GO:0006658phosphatidylserine metabolic process0.0350739049383545
GO:0045321leukocyte activation0.0350739049383545
GO:0045058T cell selection0.0366564909979633
GO:0033077T cell differentiation in the thymus0.0366564909979633
GO:0015012heparan sulfate proteoglycan biosynthetic process0.0366564909979633
GO:0005768endosome0.036817275616302
GO:0001775cell activation0.0420860864985067
GO:0002376immune system process0.043307848271674
GO:0004047aminomethyltransferase activity0.043307848271674
GO:0000209protein polyubiquitination0.043307848271674
GO:0030201heparan sulfate proteoglycan metabolic process0.043307848271674
GO:0044459plasma membrane part0.0456633991087196



Enriched sample ontology terms on this co-expression clusterSummary: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


uberon_data


Uber Anatomy
Ontology termp-valuen
thymus8.36e-344
hemolymphoid system gland8.36e-344
thymic region8.36e-344
pharyngeal gland8.36e-344
thymus primordium8.36e-344
pharyngeal epithelium6.07e-236
hemopoietic organ7.84e-207
immune organ7.84e-207
neck3.25e-1410
gland of gut3.25e-1410
chordate pharynx3.25e-1410
pharyngeal region of foregut3.25e-1410
pharynx5.10e-1311
entire pharyngeal arch endoderm5.10e-1311
early pharyngeal endoderm5.10e-1311
pharyngeal arch system2.42e-0818
upper respiratory tract5.94e-0819


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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)
MA0003.16.12504e-10
MA0004.10.0991494
MA0006.10.0190441
MA0007.10.080279
MA0009.10.849615
MA0014.11.43396e-09
MA0017.10.213269
MA0019.10.187061
MA0024.10.136822
MA0025.11.80152
MA0027.11.35099
MA0028.10.0109957
MA0029.10.350021
MA0030.10.142812
MA0031.10.241742
MA0038.10.248289
MA0040.10.156495
MA0041.10.120372
MA0042.10.1601
MA0043.11.79021
MA0046.10.217317
MA0048.10.0595018
MA0050.10.268569
MA0051.10.0166459
MA0052.10.159643
MA0055.10.0238655
MA0056.10
MA0057.10.230988
MA0058.10.0273756
MA0059.10.0576799
MA0060.10.00934551
MA0061.10.0728431
MA0063.10
MA0066.10.617623
MA0067.10.219422
MA0068.10.844214
MA0069.11.2309
MA0070.10.447645
MA0071.10.695273
MA0072.11.17435
MA0073.12.61519
MA0074.10.0538932
MA0076.10.0353414
MA0077.10.191974
MA0078.10.995289
MA0081.10.107969
MA0083.10.0662826
MA0084.10.348824
MA0087.10.196748
MA0088.10.00127407
MA0089.10
MA0090.10.0438675
MA0091.11.7325
MA0092.10.675653
MA0093.10.0424849
MA0095.10
MA0098.10
MA0100.11.57649
MA0101.10.214738
MA0103.12.28894
MA0105.10.0417379
MA0106.10.181825
MA0107.10.160699
MA0108.20.450581
MA0109.10
MA0111.10.183764
MA0113.10.837752
MA0114.10.0580633
MA0115.10.173716
MA0116.10.338362
MA0117.10.0771297
MA0119.11.28253
MA0122.10.612822
MA0124.10.460091
MA0125.12.34911
MA0130.10
MA0131.10.0106018
MA0132.10
MA0133.10
MA0135.11.39795
MA0136.10.428948
MA0139.10.229114
MA0140.10.475458
MA0141.10.397418
MA0142.10.646184
MA0143.10.0949979
MA0144.10.433199
MA0145.10.000394851
MA0146.15.93745e-06
MA0147.10.258508
MA0148.10.0614612
MA0149.10.00133915
MA0062.20.140069
MA0035.20.681243
MA0039.23.97825e-05
MA0138.21.34649
MA0002.24.86868
MA0137.20.106213
MA0104.20.056464
MA0047.20.0241237
MA0112.20.00583391
MA0065.20.0548432
MA0150.10.509889
MA0151.10
MA0152.10.711728
MA0153.10.68314
MA0154.10.0780949
MA0155.10.127789
MA0156.10.876018
MA0157.10.17131
MA0158.10
MA0159.10.260941
MA0160.10.260131
MA0161.10
MA0162.11.04669e-07
MA0163.10.00146932
MA0164.10.0361692
MA0080.21.35023
MA0018.20.0277361
MA0099.20.0963406
MA0079.24.53825e-09
MA0102.20.377001
MA0258.10.928585
MA0259.10.0130797
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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


No analysis results for this cluster

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

link to data source
data