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Coexpression cluster:C4520

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Full id: C4520_Wilms_hepatocellular_iPS_choriocarcinoma_testicular_alveolar_gastric



Phase1 CAGE Peaks

Hg19::chr5:74162605..74162621,-p4@FAM169A
Hg19::chr5:74162739..74162777,-p5@FAM169A
Hg19::chr5:74162783..74162811,-p8@FAM169A


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
embryonic stem cell5.32e-125
germ line cell2.52e-117
germ cell2.52e-117
Uber Anatomy
Ontology termp-valuen
neural tube2.61e-4456
neural rod2.61e-4456
future spinal cord2.61e-4456
neural keel2.61e-4456
regional part of nervous system6.05e-4253
regional part of brain6.05e-4253
central nervous system8.69e-3781
regional part of forebrain6.01e-3641
forebrain6.01e-3641
anterior neural tube6.01e-3641
future forebrain6.01e-3641
nervous system1.38e-3389
brain7.37e-3268
future brain7.37e-3268
adult organism3.87e-31114
telencephalon9.50e-3034
brain grey matter2.52e-2934
gray matter2.52e-2934
neural plate2.31e-2882
presumptive neural plate2.31e-2882
neurectoderm4.29e-2886
cerebral hemisphere1.76e-2632
regional part of telencephalon2.46e-2632
regional part of cerebral cortex4.27e-2322
pre-chordal neural plate4.48e-2361
neocortex1.22e-2220
ecto-epithelium2.92e-21104
cerebral cortex7.23e-2025
pallium7.23e-2025
structure with developmental contribution from neural crest1.42e-15132
organ system subdivision5.93e-15223
ectoderm-derived structure2.90e-14171
ectoderm2.90e-14171
presumptive ectoderm2.90e-14171
male reproductive organ5.56e-1211
neural nucleus4.29e-119
nucleus of brain4.29e-119
occipital lobe7.89e-115
tube8.79e-10192
testis1.20e-098
corpus striatum1.36e-094
striatum1.36e-094
ventral part of telencephalon1.36e-094
future corpus striatum1.36e-094
posterior neural tube1.48e-0915
chordal neural plate1.48e-0915
gyrus2.01e-096
basal ganglion2.39e-089
nuclear complex of neuraxis2.39e-089
aggregate regional part of brain2.39e-089
collection of basal ganglia2.39e-089
cerebral subcortex2.39e-089
brainstem2.96e-086
telencephalic nucleus5.15e-087
caudate-putamen1.17e-073
dorsal striatum1.17e-073
diencephalon1.52e-077
future diencephalon1.52e-077
temporal lobe1.86e-076
segmental subdivision of hindbrain1.99e-0712
hindbrain1.99e-0712
presumptive hindbrain1.99e-0712
anatomical conduit2.79e-07240
segmental subdivision of nervous system9.00e-0713
Disease
Ontology termp-valuen
germ cell and embryonal cancer1.31e-0722
germ cell cancer1.31e-0722


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.14.00868
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
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.13.42881
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
MA0090.12.97077
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.15.86045
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.13.08252
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
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.97249
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
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488362.71700033932814.049570681927e-060.000130333778875123
EP300#203336.77394172622320.003216880500103790.0168185714132129
FOXA1#3169311.08141974938550.000734755275698670.0058337468632122
FOXA2#3170324.63046375266526.68983856509345e-050.00107571986127759
HDAC2#3066313.41562023662630.0004140761399857210.00392964088904759
HNF4A#3172323.13229036295378.07584663437677e-050.0012330896880814
HNF4G#3174328.75342252644684.20470658818262e-050.000759749742842915
RXRA#6256320.07461713913330.0001235730348432220.00165820945470786
SP1#666735.69838137814090.005403962701712170.0247645660642438
TCF7L2#6934310.77017656313730.0008003181298398380.00616722682523005



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.