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Coexpression cluster:C4664

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Full id: C4664_teratocarcinoma_iPS_HES3GFP_Neural_H9_Lens_hepatoblastoma



Phase1 CAGE Peaks

  Short description
Hg19::chr7:148036524..148036538,+ p7@CNTNAP2
Hg19::chr7:148036546..148036559,+ p4@CNTNAP2
Hg19::chr7:148036562..148036609,+ p3@CNTNAP2


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


Cell Type
Ontology termp-valuen
neuronal stem cell2.06e-098
ectodermal cell7.19e-0972
neural cell8.26e-0925
germ line cell1.55e-077
germ cell1.55e-077
B cell1.63e-0714
neuron3.05e-076
neuroblast3.05e-076
electrically signaling cell3.05e-076
endodermal cell4.79e-0758
embryonic stem cell5.77e-075
Uber Anatomy
Ontology termp-valuen
central nervous system1.01e-3381
nervous system2.64e-3289
organ system subdivision2.42e-27223
brain4.86e-2568
future brain4.86e-2568
neural tube2.61e-2456
neural rod2.61e-2456
future spinal cord2.61e-2456
neural keel2.61e-2456
regional part of nervous system8.48e-2353
regional part of brain8.48e-2353
neurectoderm1.73e-2286
neural plate2.36e-2182
presumptive neural plate2.36e-2182
ectoderm-derived structure7.60e-21171
ectoderm7.60e-21171
presumptive ectoderm7.60e-21171
regional part of forebrain1.15e-1941
forebrain1.15e-1941
anterior neural tube1.15e-1941
future forebrain1.15e-1941
pre-chordal neural plate1.16e-1961
ecto-epithelium3.95e-19104
anatomical cluster1.35e-18373
cerebral hemisphere3.57e-1732
brain grey matter4.99e-1734
gray matter4.99e-1734
telencephalon7.66e-1734
regional part of telencephalon8.63e-1632
cerebral cortex6.65e-1325
pallium6.65e-1325
adult organism6.98e-13114
regional part of cerebral cortex8.18e-1122
structure with developmental contribution from neural crest6.22e-10132
neocortex1.45e-0920
embryo2.60e-08592
tube2.79e-08192
multi-tissue structure3.22e-08342
anatomical conduit6.78e-08240
Disease
Ontology termp-valuen
germ cell and embryonal cancer2.03e-0922
germ cell cancer2.03e-0922


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
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.10.118426
MA0017.11.64148
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
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.12.0778
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
MA0113.11.00436
MA0114.11.35563
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
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
CTBP2#1488362.71700033932814.049570681927e-060.000130494635127977
E2F1#186934.907389214879320.008460985347239390.0327607922248298
EP300#203336.77394172622320.003216880500103790.0168438675699559
HDAC2#3066313.41562023662630.0004140761399857210.0039350043661482
JUND#372736.994663941871030.002921845042734990.0157645593024849
MYC#460935.22228187160940.007020843755740150.0295999475619952
RFX5#5993312.04791082719510.0005717246050312580.00486795581484262
SP1#666735.69838137814090.005403962701712170.0247852294850519
TAF7#6879311.43306940492390.0006690181981945830.0054561605186041
TCF7L2#6934310.77017656313730.0008003181298398380.00617223638770808
TRIM28#10155318.59052504526250.0001555969297255280.00198078836465192
YY1#752834.911170749853860.008441455341808260.0331173567650769
ZEB1#6935316.88843201754390.0002075486917327580.00243744268704346



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.