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{{Coexpression_clusters
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|full_id=C3357_extraskeletal_uterus_cerebellum_small_gastric_mesothelioma_mesodermal
|id=C3357
}}

Latest revision as of 12:24, 17 September 2013


Full id: C3357_extraskeletal_uterus_cerebellum_small_gastric_mesothelioma_mesodermal



Phase1 CAGE Peaks

Hg19::chr13:22245205..22245220,+p1@FGF9
Hg19::chr13:22245257..22245270,+p3@FGF9
Hg19::chr13:22245274..22245305,+p2@FGF9


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><br>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell5.03e-0818
alpha-beta T cell5.03e-0818
immature T cell5.03e-0818
mature T cell5.03e-0818
immature alpha-beta T cell5.03e-0818
T cell4.56e-0725
pro-T cell4.56e-0725
Uber Anatomy
Ontology termp-valuen
neural tube2.36e-3556
neural rod2.36e-3556
future spinal cord2.36e-3556
neural keel2.36e-3556
regional part of nervous system1.28e-3453
regional part of brain1.28e-3453
adult organism8.45e-33114
regional part of forebrain6.22e-2941
forebrain6.22e-2941
anterior neural tube6.22e-2941
future forebrain6.22e-2941
brain grey matter2.20e-2734
gray matter2.20e-2734
telencephalon6.44e-2734
cerebral hemisphere2.45e-2632
regional part of telencephalon1.65e-2532
neural plate5.37e-2482
presumptive neural plate5.37e-2482
neurectoderm1.17e-2386
brain1.49e-2368
future brain1.49e-2368
central nervous system5.14e-2381
regional part of cerebral cortex2.92e-2122
cerebral cortex2.83e-2025
pallium2.83e-2025
neocortex1.33e-1920
nervous system1.71e-1989
pre-chordal neural plate1.49e-1861
ecto-epithelium3.62e-17104
organ system subdivision1.30e-13223
structure with developmental contribution from neural crest2.85e-12132
organ part3.13e-10218
ectoderm-derived structure6.69e-09171
ectoderm6.69e-09171
presumptive ectoderm6.69e-09171
neural nucleus1.56e-089
nucleus of brain1.56e-089
basal ganglion5.35e-089
nuclear complex of neuraxis5.35e-089
aggregate regional part of brain5.35e-089
collection of basal ganglia5.35e-089
cerebral subcortex5.35e-089
posterior neural tube9.60e-0815
chordal neural plate9.60e-0815
gyrus2.10e-076
brainstem3.78e-076
temporal lobe4.28e-076
segmental subdivision of hindbrain5.43e-0712
hindbrain5.43e-0712
presumptive hindbrain5.43e-0712
tube7.43e-07192


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0055.11.67416
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
MA0088.12.84236
MA0089.10
MA0090.10.751469
MA0091.11.93651
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
MA0116.11.3784
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
MA0144.12.26598
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
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
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139036383469521
CCNT2#90536.336201576962630.003930750035764890.0189521999439199
CTCF#1066435.360256373075030.0064925092527670.0278720475932972
E2F1#186934.907389214879320.008460985347239390.0324170677090258
E2F6#187635.017155731697390.00791769806886330.0321095200020974
EBF1#187938.9064668465690.00141523283560980.00913281649272444
EGR1#195834.988179094810140.008056488137383440.0319600244836172
ELF1#199734.258097958807540.01295179875054610.0460782432793393
ESR1#2099330.76860329615453.43136389821584e-050.000674765984119307
FOSL1#8061339.7135797163731.59554825631833e-050.000370552511322282
GABPB1#255337.067683836182170.002832212825417420.0153786770964838
HMGN3#932438.178547723350590.001827766942164210.0108472639886742
MYC#460935.22228187160940.007020843755740150.0293640583479134
NANOG#79923329.24477848101273.99627955670032e-050.000735708515110568
NRF1#4899312.21027944771090.0005492172401020010.00470122935325079
PAX5#507936.669565531177830.003370290999677260.0172535572626486
SP1#666735.69838137814090.005403962701712170.0245812047301445
SUZ12#23512350.11578091106297.93834897779404e-060.000221677333928297
TCF12#6938310.63446490218640.0008313523990202070.00628351521213427
TCF7L2#6934310.77017656313730.0008003181298398380.00612340111079435
YY1#752834.911170749853860.008441455341808260.0328459131344999
ZEB1#6935316.88843201754390.0002075486917327580.00242273139777328
ZNF143#7702313.50087655222790.0004062804962997170.00388282656964185
ZNF263#1012738.221841637010680.001799043925565870.0109099029463578



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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