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Coexpression cluster:C2566

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Full id: C2566_Lens_gall_papillotubular_anaplastic_Ciliary_osteoclastoma_alveolar



Phase1 CAGE Peaks

  Short description
Hg19::chr1:218518669..218518689,+ p1@TGFB2
Hg19::chr1:218518858..218518869,+ p21@TGFB2
Hg19::chr1:218518942..218518953,+ p28@TGFB2
Hg19::chr1:218519057..218519070,+ p11@TGFB2


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


No results for this coexpression

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


No GOStat results

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
anatomical cluster3.12e-24373
cell layer1.17e-20309
anatomical conduit3.70e-20240
epithelium2.68e-19306
tube2.37e-18192
multi-tissue structure9.08e-18342
structure with developmental contribution from neural crest9.19e-18132
brain1.59e-1768
future brain1.59e-1768
central nervous system2.45e-1781
neural plate5.88e-1782
presumptive neural plate5.88e-1782
neurectoderm1.50e-1686
nervous system2.00e-1589
ectoderm-derived structure1.46e-14171
ectoderm1.46e-14171
presumptive ectoderm1.46e-14171
ecto-epithelium2.57e-14104
neural tube6.28e-1456
neural rod6.28e-1456
future spinal cord6.28e-1456
neural keel6.28e-1456
regional part of nervous system2.56e-1353
regional part of brain2.56e-1353
pre-chordal neural plate8.63e-1261
organ system subdivision2.55e-11223
regional part of forebrain2.18e-1041
forebrain2.18e-1041
anterior neural tube2.18e-1041
future forebrain2.18e-1041
brain grey matter7.51e-1034
gray matter7.51e-1034
telencephalon7.73e-1034
cerebral hemisphere2.61e-0932
embryo2.68e-09592
regional part of telencephalon3.71e-0932
multi-cellular organism9.35e-09656
vasculature of organ2.46e-0811
epithelial tube3.76e-08117
anatomical system4.86e-08624
anatomical group6.32e-08625
developing anatomical structure7.23e-08581
embryonic structure8.45e-08564
vasculature2.60e-0778
vascular system2.60e-0778
germ layer3.02e-07560
germ layer / neural crest3.02e-07560
embryonic tissue3.02e-07560
presumptive structure3.02e-07560
germ layer / neural crest derived structure3.02e-07560
epiblast (generic)3.02e-07560
cerebral cortex4.82e-0725
pallium4.82e-0725
organ part9.47e-07218


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)
MA0003.10.0214529
MA0004.11.69588
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.11.91805
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.98521
MA0058.12.50688
MA0059.13.65449
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.13.05944
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CEBPB#105135.978360719368610.007153832484726970.0297309634250856
CTBP2#1488462.71700033932816.45042639894877e-083.96047079764733e-06
CTCF#1066445.360256373075030.001211145381643620.0081770516848845
E2F6#187645.017155731697390.00157802193473060.00997379767860863
GATA2#2624412.7449317335543.78864877853583e-050.000722312321616473
GATA3#2625427.2365163572061.81561517799785e-066.77702049946094e-05
MAX#414934.839416631755340.01315737137836840.0466269454509658
TAL1#6886429.86861667744021.25525650806991e-065.04222055562743e-05
TBP#690843.706770687096390.005296377814784350.0244431463808335
USF1#739134.771124457905970.01370465887188020.0483090612906808
USF2#739239.74414803880220.001718341848410070.0107218248480165
ZNF263#1012748.221841637010680.0002187871180958320.00249072463776004



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.