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Coexpression cluster:C3917: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3917_pineal_thalamus_globus_spinal_substantia_caudate_locus
|id=C3917
}}

Latest revision as of 12:35, 17 September 2013


Full id: C3917_pineal_thalamus_globus_spinal_substantia_caudate_locus



Phase1 CAGE Peaks

Hg19::chr1:197170611..197170660,+p1@CRB1
Hg19::chr7:63767783..63767861,+p2@ZNF736
Hg19::chr7:63767903..63767927,+p4@ZNF736


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:0007163establishment and/or maintenance of cell polarity0.0236273009144786
GO:0016324apical plasma membrane0.0236273009144786
GO:0045177apical part of cell0.0236273009144786
GO:0050953sensory perception of light stimulus0.0367596844460144
GO:0007601visual perception0.0367596844460144



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 organism1.50e-36114
neural tube1.12e-3056
neural rod1.12e-3056
future spinal cord1.12e-3056
neural keel1.12e-3056
regional part of nervous system1.10e-2853
regional part of brain1.10e-2853
brain7.08e-2668
future brain7.08e-2668
central nervous system1.61e-2481
regional part of forebrain1.90e-2441
forebrain1.90e-2441
anterior neural tube1.90e-2441
future forebrain1.90e-2441
neurectoderm6.13e-2486
nervous system6.49e-2489
neural plate1.19e-2282
presumptive neural plate1.19e-2282
brain grey matter8.52e-2034
gray matter8.52e-2034
telencephalon9.28e-2034
regional part of telencephalon1.57e-1832
cerebral hemisphere1.72e-1832
pre-chordal neural plate5.12e-1861
ecto-epithelium2.94e-14104
regional part of cerebral cortex3.49e-1422
cerebral cortex4.60e-1425
pallium4.60e-1425
ectoderm-derived structure6.06e-13171
ectoderm6.06e-13171
presumptive ectoderm6.06e-13171
neocortex6.24e-1320
structure with developmental contribution from neural crest3.03e-11132
organ system subdivision9.23e-11223
posterior neural tube1.82e-0715
chordal neural plate1.82e-0715
basal ganglion2.73e-079
nuclear complex of neuraxis2.73e-079
aggregate regional part of brain2.73e-079
collection of basal ganglia2.73e-079
cerebral subcortex2.73e-079
neural nucleus2.86e-079
nucleus of brain2.86e-079


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)
MA0003.10.401049
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
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
MA0073.11.36698
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0114.10.549955
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
MA0145.10.752137
MA0146.10.107247
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
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
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
E2F1#186934.907389214879320.008460985347239390.0325544079236787
E2F6#187635.017155731697390.00791769806886330.0322422298363947
EGR1#195834.988179094810140.008056488137383440.0320818837297514
ELF1#199734.258097958807540.01295179875054610.0462547158291712
EP300#203336.77394172622320.003216880500103790.0167548265784131
GATA2#2624312.7449317335540.0004829527704283790.00437004889887104
GATA3#2625327.2365163572064.94721007899563e-050.000851485948319421
MAX#414936.452555509007120.003721913834265510.0186647920357656
MYC#460935.22228187160940.007020843755740150.029467905839559
NFKB1#479035.488063424193840.006049381815655430.02697542322895
NRF1#4899312.21027944771090.0005492172401020010.00471320454716622
PAX5#507936.669565531177830.003370290999677260.017301048007633
REST#597839.650028716128020.001112636247114590.00767977113293243
SIX5#147912211.3911435703060.009873820081429030.0370779482052483
SP1#666735.69838137814090.005403962701712170.0246693094065966
TRIM28#10155212.39368336350830.008368344129438470.0329133649368993
YY1#752834.911170749853860.008441455341808260.0329613472330771
ZEB1#6935316.88843201754390.0002075486917327580.00242924776598425
ZNF263#1012738.221841637010680.001799043925565870.0109467693161369



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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