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Coexpression cluster:C3981

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Full id: C3981_Astrocyte_trachea_Chondrocyte_Ciliary_retina_Retinal_merkel



Phase1 CAGE Peaks

  Short description
Hg19::chr1:40782923..40782936,- p4@COL9A2
Hg19::chr1:40782938..40782974,- p1@COL9A2
Hg19::chr1:40782976..40782993,- p5@COL9A2


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


Cell Type
Ontology termp-valuen
neuronal stem cell3.03e-088
neural cell6.01e-0825
oligodendrocyte6.35e-077
macroglial cell6.35e-077
astrocyte6.35e-077
oligodendrocyte precursor cell6.35e-077
kidney tubule cell6.75e-0710
nephron tubule epithelial cell6.75e-0710
Uber Anatomy
Ontology termp-valuen
neural plate3.20e-4282
presumptive neural plate3.20e-4282
neurectoderm3.93e-3986
central nervous system2.50e-3781
neural tube5.02e-3656
neural rod5.02e-3656
future spinal cord5.02e-3656
neural keel5.02e-3656
nervous system2.93e-3589
ecto-epithelium6.90e-34104
regional part of nervous system2.02e-3353
regional part of brain2.02e-3353
pre-chordal neural plate2.60e-3261
ectoderm-derived structure9.55e-28171
ectoderm9.55e-28171
presumptive ectoderm9.55e-28171
brain1.81e-2768
future brain1.81e-2768
adult organism3.67e-25114
regional part of forebrain2.55e-2441
forebrain2.55e-2441
anterior neural tube2.55e-2441
future forebrain2.55e-2441
structure with developmental contribution from neural crest3.10e-23132
telencephalon2.03e-2134
brain grey matter2.77e-2134
gray matter2.77e-2134
organ system subdivision9.51e-20223
regional part of telencephalon1.47e-1932
anatomical cluster1.88e-19373
cerebral hemisphere2.08e-1932
epithelium2.84e-15306
organ part6.60e-15218
cell layer8.19e-15309
multi-tissue structure8.34e-15342
cerebral cortex5.86e-1425
pallium5.86e-1425
posterior neural tube7.30e-1315
chordal neural plate7.30e-1315
tube2.13e-12192
segmental subdivision of nervous system1.88e-1113
neocortex3.95e-1120
regional part of cerebral cortex4.54e-1122
pigment epithelium of eye1.68e-1011
segmental subdivision of hindbrain2.30e-1012
hindbrain2.30e-1012
presumptive hindbrain2.30e-1012
eye4.47e-1021
visual system4.47e-1021
anatomical conduit4.49e-10240
sense organ2.55e-0924
sensory system2.55e-0924
entire sense organ system2.55e-0924
embryo3.69e-09592
neural nucleus4.00e-099
nucleus of brain4.00e-099
camera-type eye4.09e-0920
simple eye4.09e-0920
immature eye4.09e-0920
ocular region4.09e-0920
eyeball of camera-type eye4.09e-0920
optic cup4.09e-0920
optic vesicle4.09e-0920
eye primordium4.09e-0920
cavitated compound organ1.91e-0831
face7.05e-0822
regional part of metencephalon1.31e-079
metencephalon1.31e-079
future metencephalon1.31e-079
telencephalic nucleus2.30e-077
brainstem3.18e-076
basal ganglion3.86e-079
nuclear complex of neuraxis3.86e-079
aggregate regional part of brain3.86e-079
collection of basal ganglia3.86e-079
cerebral subcortex3.86e-079
developing anatomical structure3.99e-07581
nephron tubule epithelium6.75e-0710
vasculature of eye6.82e-076
uvea6.82e-076
vasculature of head6.82e-076


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)
MA0003.10.708947
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.15.56064
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.12.75836
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.12.78116
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CTCF#1066435.360256373075030.0064925092527670.027973233244626
SUZ12#23512350.11578091106297.93834897779404e-060.000222749389815108
YY1#752834.911170749853860.008441455341808260.0329749085294402



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.