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Coexpression cluster:C178

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Full id: C178_spleen_liver_Hepatocyte_b_lymph_vein_thymus



Phase1 CAGE Peaks

  Short description
Hg19::chr10:102890767..102890780,+ p4@TLX1
Hg19::chr10:102891007..102891008,+ p9@TLX1
Hg19::chr10:98014908..98014919,- p@chr10:98014908..98014919
-
Hg19::chr10:98014943..98014960,- p@chr10:98014943..98014960
-
Hg19::chr11:1891326..1891337,- p@chr11:1891326..1891337
-
Hg19::chr11:1891472..1891476,+ p48@LSP1
Hg19::chr11:1891482..1891489,+ p42@LSP1
Hg19::chr11:56859569..56859572,- p@chr11:56859569..56859572
-
Hg19::chr11:56859584..56859589,- p@chr11:56859584..56859589
-
Hg19::chr11:925449..925458,+ p17@AP2A2
Hg19::chr12:101869096..101869118,+ p1@SPIC
Hg19::chr12:101882023..101882028,+ p@chr12:101882023..101882028
+
Hg19::chr12:120168462..120168466,- p@chr12:120168462..120168466
-
Hg19::chr12:57388270..57388282,+ p1@GPR182
Hg19::chr12:57388297..57388302,+ p3@GPR182
Hg19::chr12:57388350..57388361,+ p2@GPR182
Hg19::chr12:72481040..72481051,+ p19@TRHDE
Hg19::chr12:72481055..72481060,+ p28@TRHDE
Hg19::chr14:24168655..24168686,+ p@chr14:24168655..24168686
+
Hg19::chr14:75904485..75904519,+ p12@JDP2
Hg19::chr14:81859777..81859783,- p@chr14:81859777..81859783
-
Hg19::chr15:94899297..94899314,+ p16@MCTP2
Hg19::chr16:31404650..31404662,+ p1@ITGAD
Hg19::chr17:72313080..72313103,- p@chr17:72313080..72313103
-
Hg19::chr17:72313399..72313408,- p@chr17:72313399..72313408
-
Hg19::chr17:73836893..73836935,- p@chr17:73836893..73836935
-
Hg19::chr17:78945208..78945214,- p1@ENST00000545206
p1@uc002jyv.1
Hg19::chr19:14223454..14223463,- p9@PRKACA
Hg19::chr1:157801226..157801230,- p8@CD5L
Hg19::chr1:157801262..157801284,- p10@CD5L
Hg19::chr1:157811525..157811541,- p3@CD5L
Hg19::chr1:157811550..157811559,- p5@CD5L
Hg19::chr1:157811563..157811585,- p2@CD5L
Hg19::chr1:157811590..157811604,- p1@CD5L
Hg19::chr1:157811612..157811617,- p6@CD5L
Hg19::chr1:157811628..157811640,- p4@CD5L
Hg19::chr1:157811772..157811796,- p7@CD5L
Hg19::chr1:25890126..25890172,+ p9@LDLRAP1
Hg19::chr21:28820892..28820899,- p4@ENST00000420186
p4@uc002ymh.2
Hg19::chr21:28820911..28820933,- p1@ENST00000420186
p1@uc002ymh.2
Hg19::chr21:28820941..28820952,- p2@ENST00000420186
p2@uc002ymh.2
Hg19::chr21:28820954..28820963,- p3@ENST00000420186
p3@uc002ymh.2
Hg19::chr21:40181520..40181558,+ p11@ETS2
Hg19::chr21:40364741..40364783,- -
p@chr21:40364741..40364783
Hg19::chr22:36718586..36718593,- p@chr22:36718586..36718593
-
Hg19::chr2:1098240..1098249,+ p3@SNTG2
Hg19::chr2:128321491..128321509,+ p@chr2:128321491..128321509
+
Hg19::chr2:1418171..1418194,+ p2@TPO
Hg19::chr2:1418195..1418210,+ p6@TPO
Hg19::chr2:1507506..1507512,+ p16@TPO
Hg19::chr2:1508349..1508357,+ p@chr2:1508349..1508357
+
Hg19::chr2:1545753..1545760,- -
p@chr2:1545753..1545760
Hg19::chr2:218142645..218142648,+ p@chr2:218142645..218142648
+
Hg19::chr2:218142682..218142730,+ p@chr2:218142682..218142730
+
Hg19::chr2:218844734..218844743,- p@chr2:218844734..218844743
-
Hg19::chr2:218844745..218844765,- p@chr2:218844745..218844765
-
Hg19::chr3:119466528..119466536,+ p4@C3orf15
Hg19::chr3:119466639..119466644,+ p@chr3:119466639..119466644
+
Hg19::chr3:119466654..119466656,+ p@chr3:119466654..119466656
+
Hg19::chr3:119466669..119466679,+ p@chr3:119466669..119466679
+
Hg19::chr3:46505137..46505149,- p4@LTF
Hg19::chr3:46620614..46620623,+ p8@TDGF1
Hg19::chr4:185269050..185269068,- p1@ENST00000511465
Hg19::chr4:186854504..186854528,- p34@SORBS2
Hg19::chr4:76901930..76901942,+ p1@ENST00000501239
Hg19::chr5:1501865..1501869,- p@chr5:1501865..1501869
-
Hg19::chr5:1501872..1501883,- p@chr5:1501872..1501883
-
Hg19::chr5:1501941..1501953,- p@chr5:1501941..1501953
-
Hg19::chr5:152069112..152069147,- p1@ENST00000506723
p1@uc003luw.1
Hg19::chr5:76249436..76249479,+ p2@CRHBP
Hg19::chr5:76249493..76249508,+ p6@CRHBP
Hg19::chr6:36172477..36172497,+ p@chr6:36172477..36172497
+
Hg19::chr6:56707958..56707979,- p44@DST
Hg19::chr7:100420483..100420489,- p12@EPHB4
Hg19::chr7:151070957..151070988,+ p@chr7:151070957..151070988
+
Hg19::chr7:22259740..22259751,- p19@RAPGEF5
Hg19::chr7:84736120..84736124,- p@chr7:84736120..84736124
-
Hg19::chr8:22424709..22424716,- p2@ENST00000517384
Hg19::chr8:22424743..22424759,- p1@ENST00000517384
Hg19::chr8:22436248..22436259,+ p11@PDLIM2
Hg19::chr8:47834174..47834213,+ p1@ENST00000524012
Hg19::chr9:124516729..124516752,+ p@chr9:124516729..124516752
+
Hg19::chr9:126579213..126579224,- p@chr9:126579213..126579224
-
Hg19::chr9:127260615..127260651,- p@chr9:127260615..127260651
-
Hg19::chr9:127263337..127263341,- p9@NR5A1
Hg19::chr9:127267367..127267383,+ p@chr9:127267367..127267383
+
Hg19::chr9:127269434..127269438,- p8@NR5A1
Hg19::chr9:127269462..127269484,- p2@NR5A1
Hg19::chr9:127269488..127269495,- p5@NR5A1
Hg19::chr9:133973310..133973321,+ p18@AIF1L
Hg19::chr9:133973327..133973338,+ p17@AIF1L
Hg19::chr9:138596697..138596714,+ p@chr9:138596697..138596714
+
Hg19::chr9:79223787..79223821,+ p@chr9:79223787..79223821
+
Hg19::chr9:79894775..79894780,+ p12@VPS13A
Hg19::chr9:79894790..79894797,+ p10@VPS13A
Hg19::chrX:69645652..69645664,+ p7@GDPD2


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

p.valueFDRnGenesnPathwayName
7.1885277451996e-050.0455033806271134213{ETS1,13} (Static Module):NA



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:0030669clathrin-coated endocytic vesicle membrane0.000992071849670377
GO:0030128clathrin coat of endocytic vesicle0.000992071849670377
GO:0030122AP-2 adaptor complex0.000992071849670377
GO:0030666endocytic vesicle membrane0.00111553331382684
GO:0045334clathrin-coated endocytic vesicle0.0012487844173176
GO:0030132clathrin coat of coated pit0.00385392387092292
GO:0005886plasma membrane0.00578149704885549
GO:0030125clathrin vesicle coat0.00746363347430808
GO:0030139endocytic vesicle0.00746363347430808
GO:0030665clathrin coated vesicle membrane0.00746363347430808
GO:0048731system development0.00890381700236304
GO:0009986cell surface0.00896187838544101
GO:0044459plasma membrane part0.0108793621863433
GO:0005905coated pit0.0173244936324337
GO:0043565sequence-specific DNA binding0.0173244936324337
GO:0030120vesicle coat0.0173244936324337
GO:0030662coated vesicle membrane0.0173244936324337
GO:0048856anatomical structure development0.0173244936324337
GO:0035103sterol regulatory element binding protein cleavage0.0173244936324337
GO:0048645organ formation0.0173244936324337
GO:0006992sterol depletion response, sterol regulatory element binding protein cleavage0.0173244936324337
GO:0017047adrenocorticotropin-releasing hormone binding0.0173244936324337
GO:0030131clathrin adaptor complex0.0173244936324337
GO:0030119AP-type membrane coat adaptor complex0.0173244936324337
GO:0044464cell part0.0192221274731382
GO:0030118clathrin coat0.0228993724109768
GO:0006968cellular defense response0.0228993724109768
GO:0030967ER-nuclear sterol response pathway0.0228993724109768
GO:0007538primary sex determination0.0228993724109768
GO:0004447iodide peroxidase activity0.0228993724109768
GO:0016013syntrophin complex0.0228993724109768
GO:0016921pyroglutamyl-peptidase II activity0.0228993724109768
GO:0017034Rap guanyl-nucleotide exchange factor activity0.0228993724109768
GO:0015460transport accessory protein activity0.0228993724109768
GO:0007275multicellular organismal development0.0240168502532878
GO:0048513organ development0.025140756393618
GO:0042445hormone metabolic process0.0295648481646199
GO:0032933SREBP-mediated signaling pathway0.0299338749298829
GO:0006991response to sterol depletion0.0299338749298829
GO:0030659cytoplasmic vesicle membrane0.0361852549088417
GO:0048260positive regulation of receptor-mediated endocytosis0.0361852549088417
GO:0048536spleen development0.0361852549088417
GO:0016920pyroglutamyl-peptidase activity0.0361852549088417
GO:0044433cytoplasmic vesicle part0.0364903709871873
GO:0032502developmental process0.0373887191819808
GO:0012506vesicle membrane0.0373887191819808
GO:0030136clathrin-coated vesicle0.0373887191819808
GO:0030117membrane coat0.0373887191819808
GO:0048475coated membrane0.0373887191819808
GO:0030121AP-1 adaptor complex0.0373887191819808
GO:0050810regulation of steroid biosynthetic process0.0373887191819808
GO:0001784phosphotyrosine binding0.0373887191819808
GO:0007165signal transduction0.040892928832658
GO:0005856cytoskeleton0.0424029754600826
GO:0045309protein phosphorylated amino acid binding0.0424029754600826
GO:0003779actin binding0.0424971396615758
GO:0044421extracellular region part0.0424971396615758
GO:0007350blastoderm segmentation0.0424971396615758
GO:0008242omega peptidase activity0.0424971396615758
GO:0000578embryonic axis specification0.0424971396615758
GO:0008595determination of anterior/posterior axis, embryo0.0424971396615758
GO:0006895Golgi to endosome transport0.0424971396615758
GO:0007351tripartite regional subdivision0.0424971396615758
GO:0048259regulation of receptor-mediated endocytosis0.0424971396615758
GO:0005515protein binding0.0426672972879588
GO:0003700transcription factor activity0.044239107836448
GO:0030135coated vesicle0.0444686533011773
GO:0046890regulation of lipid biosynthetic process0.0450314997123685
GO:0004691cAMP-dependent protein kinase activity0.0450314997123685
GO:0048646anatomical structure formation0.0459858650514926
GO:0017046peptide hormone binding0.0485310207523525
GO:0006590thyroid hormone generation0.0485310207523525



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


uberon_data



Uber Anatomy
Ontology termp-valuen
spleen8.98e-1313
gastrointestinal system mesentery8.98e-1313
stomach region8.98e-1313
mesentery8.98e-1313
gastrointestinal system serosa8.98e-1313
mesentery of stomach8.98e-1313
gut mesentery8.98e-1313
dorsal mesentery8.98e-1313
dorsal mesogastrium8.98e-1313
peritoneal cavity8.98e-1313
spleen primordium8.98e-1313
hemopoietic organ4.76e-577
immune organ4.76e-577
stomach3.99e-508
food storage organ3.99e-508
cavity lining5.98e-3412
serous membrane5.98e-3412
intraembryonic coelom5.98e-3412
viscus3.88e-2318
gastrointestinal system1.86e-1625
mixed endoderm/mesoderm-derived structure6.74e-1529
body cavity7.07e-1046
body cavity or lining2.38e-0949
abdomen element1.34e-0854
body cavity precursor1.34e-0854
abdominal segment element1.34e-0854
abdominal segment of trunk7.34e-0860
abdomen7.34e-0860
anatomical cavity9.44e-0861
organ component layer2.96e-0766


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)
MA0003.12.37973e-06
MA0004.10.0510273
MA0006.10.138753
MA0007.10.100611
MA0009.10.104557
MA0014.10.000804284
MA0017.10.67801
MA0019.10.174179
MA0024.10.225923
MA0025.10.172989
MA0027.11.45992
MA0028.10.0957352
MA0029.10.5256
MA0030.10.233797
MA0031.10.693205
MA0038.10.12735
MA0040.10.536629
MA0041.10.0193691
MA0042.10.105931
MA0043.10.104699
MA0046.10.672622
MA0048.10.242728
MA0050.10.0445169
MA0051.10.0439353
MA0052.10.0734046
MA0055.10.137512
MA0056.10
MA0057.10.00958141
MA0058.10.0148333
MA0059.10.166782
MA0060.12.32509e-05
MA0061.10.806243
MA0063.10
MA0066.10.0457912
MA0067.10.29136
MA0068.10.00975372
MA0069.10.664698
MA0070.10.0932274
MA0071.10.36165
MA0072.10.0913317
MA0073.19.64327e-17
MA0074.10.122682
MA0076.10.10897
MA0077.10.296626
MA0078.10.724095
MA0081.11.9624
MA0083.10.710884
MA0084.10.433394
MA0087.10.627868
MA0088.10.235068
MA0089.10
MA0090.11.27199
MA0091.10.123019
MA0092.10.293752
MA0093.10.0388727
MA0095.10
MA0098.10
MA0100.10.0514378
MA0101.10.903059
MA0103.10.797848
MA0105.11.05689
MA0106.10.852652
MA0107.10.329452
MA0108.20.17034
MA0109.10
MA0111.10.591943
MA0113.10.612597
MA0114.10.428831
MA0115.10.23924
MA0116.10.238313
MA0117.10.122163
MA0119.10.0732631
MA0122.11.34628
MA0124.11.14776
MA0125.10.162878
MA0130.10
MA0131.10.0249926
MA0132.10
MA0133.10
MA0135.10.118667
MA0136.11.03268
MA0139.10.0047625
MA0140.10.198318
MA0141.12.29925
MA0142.10.339546
MA0143.10.916103
MA0144.110.1855
MA0145.11.11177
MA0146.10.116067
MA0147.10.055484
MA0148.12.83006
MA0149.10.0841481
MA0062.20.189804
MA0035.20.353966
MA0039.23.29867e-06
MA0138.20.236596
MA0002.20.629358
MA0137.22.93364
MA0104.20.0588411
MA0047.21.93299
MA0112.20.0862624
MA0065.20.633593
MA0150.10.0567192
MA0151.10
MA0152.10.207996
MA0153.10.153606
MA0154.10.406529
MA0155.10.359477
MA0156.10.804394
MA0157.12.73054
MA0158.10
MA0159.10.834531
MA0160.10.168919
MA0161.10
MA0162.19.90794e-09
MA0163.10.0805291
MA0164.10.964009
MA0080.21.11307
MA0018.20.569786
MA0099.20.0330469
MA0079.22.67119e-14
MA0102.20.463601
MA0258.10.0912015
MA0259.10.00491655
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

No analysis results for this cluster

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