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Coexpression cluster:C1101: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1101_testis_cerebellum_parietal_medial_occipital_middle_pituitary
|id=C1101
}}

Latest revision as of 11:37, 17 September 2013


Full id: C1101_testis_cerebellum_parietal_medial_occipital_middle_pituitary



Phase1 CAGE Peaks

Hg19::chr10:102279586..102279637,-p2@SEC31B
Hg19::chr10:94050794..94050818,-p2@CPEB3
Hg19::chr10:94050820..94050868,-p1@CPEB3
Hg19::chr15:76352095..76352145,-p2@NRG4
Hg19::chr18:76829258..76829280,+p3@ATP9B
Hg19::chr3:197476560..197476577,-p5@KIAA0226
Hg19::chr3:197476580..197476657,-p2@KIAA0226


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

GO IDGO nameFDR corrected p-value
GO:0015917aminophospholipid transport0.0261368651156931
GO:0004012phospholipid-translocating ATPase activity0.0478773993503692
GO:0015247aminophospholipid transporter activity0.0478773993503692
GO:0015914phospholipid transport0.0478773993503692



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.09e-56114
neural tube5.86e-3156
neural rod5.86e-3156
future spinal cord5.86e-3156
neural keel5.86e-3156
regional part of nervous system6.56e-2953
regional part of brain6.56e-2953
central nervous system1.39e-2481
nervous system7.93e-2489
brain1.22e-2368
future brain1.22e-2368
regional part of forebrain2.56e-2341
forebrain2.56e-2341
anterior neural tube2.56e-2341
future forebrain2.56e-2341
neurectoderm1.85e-2186
neural plate3.18e-2182
presumptive neural plate3.18e-2182
brain grey matter8.96e-1934
gray matter8.96e-1934
telencephalon9.74e-1934
cerebral hemisphere1.90e-1732
regional part of telencephalon2.52e-1732
regional part of cerebral cortex1.76e-1622
organ system subdivision3.58e-15223
neocortex3.87e-1520
pre-chordal neural plate4.70e-1561
structure with developmental contribution from neural crest2.32e-13132
ectoderm-derived structure5.35e-13171
ectoderm5.35e-13171
presumptive ectoderm5.35e-13171
ecto-epithelium6.56e-13104
cerebral cortex8.79e-1325
pallium8.79e-1325
posterior neural tube9.71e-0915
chordal neural plate9.71e-0915
basal ganglion1.11e-079
nuclear complex of neuraxis1.11e-079
aggregate regional part of brain1.11e-079
collection of basal ganglia1.11e-079
cerebral subcortex1.11e-079
neural nucleus1.20e-079
nucleus of brain1.20e-079
segmental subdivision of hindbrain7.81e-0712
hindbrain7.81e-0712
presumptive hindbrain7.81e-0712


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)
MA0003.12.0712
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.13.71689
MA0017.10.380797
MA0019.11.57204
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.12.23229
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.126287
MA0074.10.60198
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.11.37625
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.695228
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.980834
MA0146.11.97205
MA0147.11.40486
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.21.4671
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.21.19136
MA0047.20.636643
MA0112.20.0758925
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.13.67778
MA0163.10.942271
MA0164.10.678332
MA0080.20.344472
MA0018.22.64985
MA0099.20.572
MA0079.24.76472
MA0102.21.51913
MA0258.10.245543
MA0259.11.43531
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
ATF3#46739.62707479686090.002696129551660330.0148380183509434
CTCF#1066453.828754552196450.003387371192681340.0172893001657925
CTCFL#140690411.28369963369960.0002032736265059930.00241301367113655
E2F1#186964.206333612753710.0004135232017007640.0039361966516976
E2F4#187447.238891608733970.001117741430524870.00766536195827611
ELF1#199753.041498542005380.009719562269370750.0365538841862013
GABPB1#255344.038676477818380.00980113494696150.0368420937491258
HEY1#2346252.885793602218360.01231366941853030.0446180938973002
HMGN3#932444.673455841914620.005751881099938870.0259031827086592
MYC#460953.730201336863860.003821944222306690.0188665705267045
NRF1#489958.721628176936366.71450045004423e-050.00107307683626958
PAX5#507943.811180303530190.01208261681555190.0438188908118419
RAD21#588545.917162225975040.002393184937227960.0135528598665628
SIX5#14791237.322878009482430.00586667625269160.0263293283982149
SRF#672235.913076398071920.01066868130167450.0393872673641905
ZNF143#770247.714786601273090.0008771969606613480.00654102337387623
ZNF263#1012744.698195221148960.00564122953609810.0254795818674285



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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