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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:31, 17 September 2013


Full id: C798_cerebellum_small_carcinosarcoma_argyrophil_Neural_gastric_Ciliary



Phase1 CAGE Peaks

Hg19::chr11:31816236..31816261,-p@chr11:31816236..31816261
-
Hg19::chr11:31816304..31816311,-p@chr11:31816304..31816311
-
Hg19::chr11:31819053..31819055,-p@chr11:31819053..31819055
-
Hg19::chr11:31832581..31832601,-p7@PAX6
Hg19::chr11:31832610..31832639,-p5@PAX6
Hg19::chr11:31832658..31832681,-p1@PAX6
Hg19::chr11:31832687..31832704,-p6@PAX6
Hg19::chr11:31832807..31832823,-p4@PAX6
Hg19::chr11:31832862..31832884,-p2@PAX6
Hg19::chr11:31833011..31833025,+p@chr11:31833011..31833025
+


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
oligodendrocyte5.07e-097
macroglial cell5.07e-097
astrocyte5.07e-097
oligodendrocyte precursor cell5.07e-097
neural cell1.48e-0825
Uber Anatomy
Ontology termp-valuen
neurectoderm4.89e-5586
neural plate1.25e-5382
presumptive neural plate1.25e-5382
neural tube1.78e-5056
neural rod1.78e-5056
future spinal cord1.78e-5056
neural keel1.78e-5056
nervous system4.76e-4789
regional part of nervous system5.80e-4753
regional part of brain5.80e-4753
central nervous system7.87e-4781
pre-chordal neural plate3.13e-4361
ecto-epithelium2.52e-40104
brain3.67e-4068
future brain3.67e-4068
regional part of forebrain4.13e-3441
forebrain4.13e-3441
anterior neural tube4.13e-3441
future forebrain4.13e-3441
ectoderm-derived structure8.56e-33171
ectoderm8.56e-33171
presumptive ectoderm8.56e-33171
brain grey matter2.50e-2934
gray matter2.50e-2934
telencephalon2.58e-2934
structure with developmental contribution from neural crest1.63e-28132
cerebral hemisphere1.58e-2732
regional part of telencephalon1.83e-2732
cerebral cortex2.81e-2125
pallium2.81e-2125
organ system subdivision4.72e-18223
regional part of cerebral cortex8.36e-1822
posterior neural tube3.06e-1715
chordal neural plate3.06e-1715
neocortex1.04e-1520
segmental subdivision of hindbrain6.50e-1412
hindbrain6.50e-1412
presumptive hindbrain6.50e-1412
pigment epithelium of eye7.90e-1411
segmental subdivision of nervous system1.51e-1213
adult organism4.81e-12114
eye1.74e-1121
visual system1.74e-1121
anatomical cluster4.52e-11373
regional part of metencephalon1.02e-109
metencephalon1.02e-109
future metencephalon1.02e-109
camera-type eye2.05e-1020
simple eye2.05e-1020
immature eye2.05e-1020
ocular region2.05e-1020
eyeball of camera-type eye2.05e-1020
optic cup2.05e-1020
optic vesicle2.05e-1020
eye primordium2.05e-1020
basal ganglion1.44e-099
nuclear complex of neuraxis1.44e-099
aggregate regional part of brain1.44e-099
collection of basal ganglia1.44e-099
cerebral subcortex1.44e-099
neural nucleus1.76e-099
nucleus of brain1.76e-099
sense organ1.94e-0924
sensory system1.94e-0924
entire sense organ system1.94e-0924
face4.59e-0922
organ part4.69e-09218
cerebellum2.73e-086
rhombic lip2.73e-086
anterior segment of eyeball2.98e-0814
tube9.70e-08192
telencephalic nucleus1.15e-077
epithelium2.12e-07306
brainstem2.84e-076
cell layer3.94e-07309
Disease
Ontology termp-valuen
cell type cancer8.86e-12143
disease of cellular proliferation5.16e-07239
cancer7.84e-07235


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)
MA0003.10.115024
MA0004.10.380329
MA0006.10.236135
MA0007.10.952442
MA0009.10.828613
MA0014.10.686562
MA0017.10.270554
MA0019.10.520264
MA0024.14.17606
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.174262
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.13.40375
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.00880943
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.857892
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.14293
MA0146.15.19153
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.21.11424
MA0039.20.00259594
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.0329985
MA0065.20.963081
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.10.12484
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.64451
MA0160.10.417847
MA0161.10
MA0162.10.0377269
MA0163.10.00405048
MA0164.10.544294
MA0080.22.71391
MA0018.20.517858
MA0099.20.444294
MA0079.20.000815954
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
CCNT2#90574.435341103873840.0001875292697571890.00226735001205963
CEBPB#105175.579803338077374.14051761029175e-050.000751532010255926
CTBP2#1488743.90190023752972.99349477998484e-113.4698956862024e-09
E2F4#187478.867642220699111.84731179412716e-066.85369081587377e-05
E2F6#187673.512009012188170.0008453950419482970.00637258843637951
ELF1#199772.980668571165280.002378202870469130.0134731288087294
FOS#235376.298568716226081.848304348188e-050.00041991528784078
HDAC2#306668.049372141975762.76518202234458e-050.000584600901278635
JUND#372774.896264759309729.81446965345405e-050.00139173577208023
MAX#414974.516788856304990.0001665254509713970.00204152501162128
NANOG#79923720.47134493670895.96944508093541e-094.74101045481227e-07
NFYA#4800712.89790648988141.4357468212053e-078.1272608270927e-06
NFYB#4801711.73185527747552.74641977103244e-071.40950041507055e-05
POU2F2#545276.374286840419771.70647444265859e-050.000390838781396536
SPI1#668875.743026455965913.41922598863134e-050.00067825364297563
SUZ12#23512735.0810466377441.42572395471382e-101.51322341571501e-08
TAF1#687272.34013240002170.01040839844348330.0386352973073269
TBP#690872.594739480967470.00558866901773640.0252727864708107
TRIM28#10155713.01336753168381.35067750650695e-077.68737918812423e-06
ZNF263#1012775.755289145907473.37110736015453e-050.000669217033999579



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.

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