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Coexpression cluster:C3857

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Full id: C3857_spinal_cerebellum_salivary_hippocampus_medulla_skeletal_amygdala



Phase1 CAGE Peaks

  Short description
Hg19::chr1:145039782..145039796,- p10@PDE4DIP
Hg19::chr1:145039835..145039853,- p6@PDE4DIP
Hg19::chr1:145039864..145039875,- p9@PDE4DIP


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


Uber Anatomy
Ontology termp-valuen
adult organism3.66e-27114
neural tube1.02e-2456
neural rod1.02e-2456
future spinal cord1.02e-2456
neural keel1.02e-2456
regional part of nervous system8.19e-2353
regional part of brain8.19e-2353
brain1.08e-1968
future brain1.08e-1968
central nervous system3.52e-1981
structure with developmental contribution from neural crest5.24e-19132
regional part of forebrain1.48e-1841
forebrain1.48e-1841
anterior neural tube1.48e-1841
future forebrain1.48e-1841
neural plate1.53e-1882
presumptive neural plate1.53e-1882
nervous system2.52e-1789
neurectoderm7.13e-1786
ecto-epithelium1.48e-16104
multi-cellular organism1.58e-16656
telencephalon3.12e-1634
brain grey matter3.23e-1634
gray matter3.23e-1634
organ4.72e-16503
anatomical system2.92e-15624
anatomical group3.01e-15625
regional part of telencephalon5.51e-1532
cerebral hemisphere6.05e-1532
ectoderm-derived structure1.90e-14171
ectoderm1.90e-14171
presumptive ectoderm1.90e-14171
musculoskeletal system2.25e-14167
embryonic structure4.54e-14564
germ layer6.15e-14560
germ layer / neural crest6.15e-14560
embryonic tissue6.15e-14560
presumptive structure6.15e-14560
germ layer / neural crest derived structure6.15e-14560
epiblast (generic)6.15e-14560
regional part of cerebral cortex1.47e-1222
neocortex2.04e-1120
cerebral cortex2.93e-1125
pallium2.93e-1125
pre-chordal neural plate4.15e-1161
developing anatomical structure4.92e-11581
embryo8.38e-10592
skeletal system1.17e-09100
tissue5.80e-09773
skeletal element5.90e-0990
bone element2.61e-0882
bone marrow1.06e-0776
posterior neural tube2.33e-0715
chordal neural plate2.33e-0715


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.13.9895
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
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
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
MA0113.12.29491
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
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.13.48527
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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
CCNT2#90536.336201576962630.003930750035764890.0190074823124942
CTBP2#1488362.71700033932814.049570681927e-060.000129773891515733
CTCF#1066435.360256373075030.0064925092527670.0279490199847382
E2F6#187635.017155731697390.00791769806886330.0322284070704659
EBF1#187938.9064668465690.00141523283560980.00915374386067086
EP300#203336.77394172622320.003216880500103790.0167473098325278
FOXA1#3169311.08141974938550.000734755275698670.00581341713929495
GATA3#2625327.2365163572064.94721007899563e-050.000851205392817503
HMGN3#932438.178547723350590.001827766942164210.010871975832822
MAX#414936.452555509007120.003721913834265510.0186549387597473
NRF1#4899312.21027944771090.0005492172401020010.00471243011329386
PAX5#507936.669565531177830.003370290999677260.0172942476153537
RAD21#5885310.35503389545630.0009004912073565420.00664169500036086
RFX5#5993312.04791082719510.0005717246050312580.00484583233443106
SIN3A#2594235.408884726815140.006318961977991520.0276846241303573
STAT3#6774310.51946499715420.0008589184530415310.0064267505600519
SUZ12#23512350.11578091106297.93834897779404e-060.000222331249367614
ZNF263#1012738.221841637010680.001799043925565870.0109435813700375



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.