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Coexpression cluster:C969

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Full id: C969_mature_insula_mesodermal_occipital_Preadipocyte_temporal_heart



Phase1 CAGE Peaks

  Short description
Hg19::chr10:118502070..118502084,- p1@HSPA12A
Hg19::chr15:62682733..62682759,+ p1@TLN2
Hg19::chr21:35014829..35014912,+ p1@ITSN1
Hg19::chr2:54683419..54683442,+ p2@SPTBN1
Hg19::chr2:54683448..54683470,+ p1@SPTBN1
Hg19::chr2:54684327..54684399,+ p4@SPTBN1
Hg19::chr9:131314859..131314877,+ p1@SPTAN1
Hg19::chr9:87285539..87285560,+ p21@NTRK2


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
3.79490086907914e-050.0120108612506355246Interactions of the immunoglobulin superfamily (IgSF) member proteins (Reactome):REACT_23853
1.65551775624537e-060.00104794273970332210{SPTAN1,10} (Static Module):NA



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:0005200structural constituent of cytoskeleton4.99147211879799e-05
GO:0008091spectrin9.70308090475593e-05
GO:0030864cortical actin cytoskeleton0.000136243055220067
GO:0051693actin filament capping0.000136243055220067
GO:0051016barbed-end actin filament capping0.000136243055220067
GO:0030835negative regulation of actin filament depolymerization0.000136243055220067
GO:0030834regulation of actin filament depolymerization0.000136243055220067
GO:0030042actin filament depolymerization0.000136243055220067
GO:0030863cortical cytoskeleton0.000143580142384078
GO:0015629actin cytoskeleton0.000213216949059869
GO:0008064regulation of actin polymerization and/or depolymerization0.000290516615129923
GO:0044448cell cortex part0.000290516615129923
GO:0051261protein depolymerization0.000290516615129923
GO:0030832regulation of actin filament length0.000290516615129923
GO:0032535regulation of cellular component size0.000290516615129923
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.000290516615129923
GO:0051129negative regulation of cellular component organization and biogenesis0.000335265835546014
GO:0051493regulation of cytoskeleton organization and biogenesis0.000343288446968344
GO:0033043regulation of organelle organization and biogenesis0.000343288446968344
GO:0003779actin binding0.000343288446968344
GO:0008154actin polymerization and/or depolymerization0.000374299671112961
GO:0005938cell cortex0.000393507614964763
GO:0008092cytoskeletal protein binding0.000771815799853878
GO:0051128regulation of cellular component organization and biogenesis0.000883182958994439
GO:0051248negative regulation of protein metabolic process0.000917108549270258
GO:0007010cytoskeleton organization and biogenesis0.00100030724883964
GO:0005516calmodulin binding0.00156030768475826
GO:0030036actin cytoskeleton organization and biogenesis0.00459280999558969
GO:0030029actin filament-based process0.00488493878915314
GO:0043121neurotrophin binding0.00488493878915314
GO:0048488synaptic vesicle endocytosis0.00567241467434988
GO:0016043cellular component organization and biogenesis0.00573061625175347
GO:0005856cytoskeleton0.00662604076192401
GO:0006996organelle organization and biogenesis0.00797412921710054
GO:0007016cytoskeletal anchoring0.0091139899944362
GO:0005886plasma membrane0.0091139899944362
GO:0051246regulation of protein metabolic process0.0100232053533945
GO:0030054cell junction0.0100807159878271
GO:0009892negative regulation of metabolic process0.0101401678185353
GO:0007043intercellular junction assembly0.0102515793004705
GO:0045216intercellular junction assembly and maintenance0.0125492597196398
GO:0048489synaptic vesicle transport0.0125492597196398
GO:0007028cytoplasm organization and biogenesis0.0163360075800794
GO:0044459plasma membrane part0.0196488111773652
GO:0005624membrane fraction0.0211664538902833
GO:0005925focal adhesion0.0215907385342878
GO:0005515protein binding0.0215907385342878
GO:0019717synaptosome0.0219321352358375
GO:0005924cell-substrate adherens junction0.0226747890717908
GO:0030055cell-matrix junction0.0233873930407654
GO:0001726ruffle0.0246430376281777
GO:0005912adherens junction0.0302912053126019
GO:0000267cell fraction0.0302912053126019
GO:0019538protein metabolic process0.0302912053126019
GO:0044430cytoskeletal part0.0302912053126019
GO:0043232intracellular non-membrane-bound organelle0.0302912053126019
GO:0043228non-membrane-bound organelle0.0302912053126019
GO:0065008regulation of biological quality0.0313083760599613
GO:0031252leading edge0.0355917882053961
GO:0016323basolateral plasma membrane0.0412782857834084
GO:0048523negative regulation of cellular process0.0417652213505117
GO:0019838growth factor binding0.0418142683574165
GO:0048519negative regulation of biological process0.0435488653287554
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0495374653713563



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

cell_data
uberon_data


Cell Type
Ontology termp-valuen
fibroblast3.84e-1076
mesodermal cell2.71e-07121
Uber Anatomy
Ontology termp-valuen
central nervous system8.85e-3081
anatomical cluster1.68e-29373
brain1.09e-2868
future brain1.09e-2868
adult organism1.85e-28114
neural tube1.87e-2856
neural rod1.87e-2856
future spinal cord1.87e-2856
neural keel1.87e-2856
nervous system2.30e-2889
structure with developmental contribution from neural crest7.88e-28132
regional part of nervous system8.93e-2753
regional part of brain8.93e-2753
tube2.70e-25192
anatomical conduit9.35e-25240
neural plate2.38e-2382
presumptive neural plate2.38e-2382
regional part of forebrain2.38e-2341
forebrain2.38e-2341
anterior neural tube2.38e-2341
future forebrain2.38e-2341
cell layer5.03e-22309
multi-tissue structure9.41e-22342
neurectoderm1.51e-2186
epithelium1.93e-21306
telencephalon3.81e-2034
brain grey matter4.79e-2034
gray matter4.79e-2034
cerebral hemisphere3.48e-1932
regional part of telencephalon5.71e-1932
ectoderm-derived structure6.42e-19171
ectoderm6.42e-19171
presumptive ectoderm6.42e-19171
multi-cellular organism7.08e-17656
pre-chordal neural plate7.57e-1761
ecto-epithelium2.66e-16104
organ system subdivision2.87e-16223
regional part of cerebral cortex2.80e-1522
cerebral cortex5.90e-1525
pallium5.90e-1525
anatomical system9.89e-15624
anatomical group1.65e-14625
neocortex4.48e-1420
organ part5.27e-11218
splanchnic layer of lateral plate mesoderm8.27e-1083
germ layer3.38e-09560
germ layer / neural crest3.38e-09560
embryonic tissue3.38e-09560
presumptive structure3.38e-09560
germ layer / neural crest derived structure3.38e-09560
epiblast (generic)3.38e-09560
developing anatomical structure3.86e-09581
embryonic structure4.95e-09564
embryo6.05e-09592
organ7.42e-09503
vasculature1.93e-0878
vascular system1.93e-0878
vessel3.24e-0768
epithelial tube open at both ends3.71e-0759
blood vessel3.71e-0759
blood vasculature3.71e-0759
vascular cord3.71e-0759
epithelial tube4.31e-07117
mesenchyme5.58e-07160
entire embryonic mesenchyme5.58e-07160
paraxial mesoderm6.33e-0772
presumptive paraxial mesoderm6.33e-0772
dense mesenchyme tissue7.26e-0773
primary circulatory organ8.36e-0727
basal ganglion9.59e-079
nuclear complex of neuraxis9.59e-079
aggregate regional part of brain9.59e-079
collection of basal ganglia9.59e-079
cerebral subcortex9.59e-079


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)
MA0003.14.69204
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.13.20776
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.12.19172
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.11.05663
MA0058.10.362328
MA0059.10.361075
MA0060.10.556724
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.15.03496
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.12.18672
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.586268
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.220937
MA0146.11.26525
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.23.46158
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.458158
MA0065.20.844872
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.11.70684
MA0163.11.83367
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.216.0339
MA0102.21.46209
MA0258.10.603127
MA0259.10.699589
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


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

TF#promotersEnrichmentp-valueq-value
E2F1#186953.067118259299580.01129732364974160.0414473314594218
HEY1#2346263.030083282329280.004001723466483270.0191889805838405
TAF1#687272.925165500027130.001265325357915740.0084934324220941
TAF7#687945.716534702461960.003068541555180160.0161774564099677
ZNF263#1012755.138651023131670.001082531249033560.0076401190105295



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


This analysis result is provided for C0 - C305 clusters.