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Coexpression cluster:C1905

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Full id: C1905_caudate_putamen_embryonic_pituitary_globus_cord_rhabdomyosarcoma



Phase1 CAGE Peaks

  Short description
Hg19::chr2:45168959..45168990,+ p6@SIX3
Hg19::chr2:45168997..45169020,+ p4@SIX3
Hg19::chr2:45169024..45169033,+ p12@SIX3
Hg19::chr2:45169317..45169326,+ p13@SIX3
Hg19::chr2:45169684..45169715,+ p9@SIX3


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

cell_data
uberon_data
disease_data


Uber Anatomy
Ontology termp-valuen
pre-chordal neural plate1.63e-2661
neurectoderm8.36e-2286
pigment epithelium of eye2.28e-2011
neural plate3.24e-2082
presumptive neural plate3.24e-2082
nervous system1.51e-1789
ectoderm-derived structure2.47e-17171
ectoderm2.47e-17171
presumptive ectoderm2.47e-17171
eye8.39e-1721
visual system8.39e-1721
ecto-epithelium3.18e-15104
camera-type eye5.09e-1520
simple eye5.09e-1520
immature eye5.09e-1520
ocular region5.09e-1520
eyeball of camera-type eye5.09e-1520
optic cup5.09e-1520
optic vesicle5.09e-1520
eye primordium5.09e-1520
sense organ2.87e-1424
sensory system2.87e-1424
entire sense organ system2.87e-1424
regional part of forebrain1.36e-1341
forebrain1.36e-1341
anterior neural tube1.36e-1341
future forebrain1.36e-1341
face2.26e-1322
telencephalic nucleus6.80e-137
structure with developmental contribution from neural crest7.69e-13132
diencephalon1.67e-127
future diencephalon1.67e-127
central nervous system1.68e-1281
brain2.77e-1268
future brain2.77e-1268
regional part of nervous system7.27e-1253
regional part of brain7.27e-1253
corpus striatum4.03e-114
striatum4.03e-114
ventral part of telencephalon4.03e-114
future corpus striatum4.03e-114
neural tube5.78e-1156
neural rod5.78e-1156
future spinal cord5.78e-1156
neural keel5.78e-1156
retina2.51e-106
photoreceptor array2.51e-106
posterior segment of eyeball2.51e-106
atypical epithelium5.40e-104
basal ganglion8.14e-109
neural nucleus8.14e-109
nuclear complex of neuraxis8.14e-109
nucleus of brain8.14e-109
aggregate regional part of brain8.14e-109
collection of basal ganglia8.14e-109
cerebral subcortex8.14e-109
caudate-putamen7.56e-093
dorsal striatum7.56e-093
ectodermal placode1.25e-0831
peripheral nervous system2.33e-088
pigmented layer of retina5.58e-083
presumptive retinal pigmented epithelium5.58e-083
pancreas5.62e-0810
ciliary epithelium7.05e-083
ciliary body7.05e-083
sympathetic nervous system1.31e-075
autonomic nervous system1.31e-075
anterior segment of eyeball1.48e-0714
vasculature of organ5.66e-0711
telencephalon7.66e-0734
viscus7.77e-0718
Disease
Ontology termp-valuen
neuroectodermal tumor3.52e-1010
neuroendocrine tumor2.55e-096


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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.12.53085
MA0051.14.20326
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.66737
MA0058.10.523638
MA0059.11.29682
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.16.69924
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.12.7505
MA0062.20.777733
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.22.44686
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
GATA2#2624410.19594538684320.0001775447777609820.00215762148528964
PBX3#5090313.14870761204650.0008860469322808430.00660560036836883
SUZ12#23512550.11578091106293.15480790456198e-092.62747195171092e-07
ZNF263#1012746.577473309608540.0009875103237900160.00709365091865366



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.