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Coexpression cluster:C1643: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1643_cerebellum_breast_pineal_spinal_acute_hippocampus_medulla
|id=C1643
}}

Latest revision as of 11:49, 17 September 2013


Full id: C1643_cerebellum_breast_pineal_spinal_acute_hippocampus_medulla



Phase1 CAGE Peaks

Hg19::chr11:71791726..71791756,-p8@NUMA1
Hg19::chr1:150039659..150039684,-p@chr1:150039659..150039684
-
Hg19::chr1:61547894..61547968,+p2@NFIA
Hg19::chr1:61548069..61548102,+p3@NFIA
Hg19::chr1:61548118..61548129,+p9@NFIA


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:0051322anaphase0.0108906810524625
GO:0000090mitotic anaphase0.0108906810524625
GO:0005876spindle microtubule0.0197881225581302
GO:0019079viral genome replication0.0197881225581302
GO:0000922spindle pole0.0197881225581302
GO:0043025cell soma0.0197881225581302
GO:0006997nuclear organization and biogenesis0.0197881225581302
GO:0030425dendrite0.0197881225581302
GO:0016363nuclear matrix0.0197881225581302
GO:0008017microtubule binding0.0197881225581302
GO:0019058viral infectious cycle0.0197881225581302
GO:0022415viral reproductive process0.0206764560402455
GO:0015631tubulin binding0.0220289584636577
GO:0051321meiotic cell cycle0.0220289584636577
GO:0005819spindle0.0220289584636577
GO:0043005neuron projection0.0220289584636577



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 organism2.97e-51114
neural tube2.20e-3156
neural rod2.20e-3156
future spinal cord2.20e-3156
neural keel2.20e-3156
organ system subdivision2.63e-31223
regional part of nervous system1.69e-2953
regional part of brain1.69e-2953
central nervous system2.60e-2981
nervous system3.74e-2989
brain3.49e-2768
future brain3.49e-2768
neurectoderm2.38e-2686
neural plate9.80e-2682
presumptive neural plate9.80e-2682
anatomical cluster1.18e-24373
regional part of forebrain3.83e-2441
forebrain3.83e-2441
anterior neural tube3.83e-2441
future forebrain3.83e-2441
ecto-epithelium4.82e-21104
ectoderm-derived structure5.76e-21171
ectoderm5.76e-21171
presumptive ectoderm5.76e-21171
brain grey matter2.53e-2034
gray matter2.53e-2034
telencephalon3.11e-2034
regional part of telencephalon4.74e-1932
cerebral hemisphere6.66e-1932
structure with developmental contribution from neural crest3.41e-18132
pre-chordal neural plate7.04e-1861
multi-tissue structure7.20e-18342
anatomical conduit7.64e-17240
cerebral cortex5.28e-1525
pallium5.28e-1525
tube1.58e-14192
regional part of cerebral cortex1.92e-1422
cell layer2.36e-14309
epithelium3.04e-14306
neocortex2.64e-1320
germ layer7.25e-13560
germ layer / neural crest7.25e-13560
embryonic tissue7.25e-13560
presumptive structure7.25e-13560
germ layer / neural crest derived structure7.25e-13560
epiblast (generic)7.25e-13560
embryonic structure2.01e-12564
developing anatomical structure6.26e-12581
multi-cellular organism2.82e-11656
embryo1.17e-10592
anatomical system2.59e-09624
anatomical group4.95e-09625
organ part5.79e-09218
posterior neural tube2.29e-0815
chordal neural plate2.29e-0815
subdivision of digestive tract3.80e-08118
organ1.34e-07503
digestive system1.36e-07145
digestive tract1.36e-07145
primitive gut1.36e-07145
segmental subdivision of nervous system2.91e-0713
endoderm-derived structure6.78e-07160
endoderm6.78e-07160
presumptive endoderm6.78e-07160
neural nucleus8.55e-079
nucleus of brain8.55e-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)
MA0003.11.04569
MA0004.10.626788
MA0006.10.452993
MA0007.11.47524
MA0009.11.11255
MA0014.11.45664
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.28241
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.123.9233
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.11.35428
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.22.8814
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.20.839774
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.14.96327
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.217.7775
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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#90545.068961261570110.002709998091280770.0148892361857684
CHD2#110648.275218267293490.0004028373567101730.00387652544894994
E2F1#186954.907389214879320.0003512818099256460.00352222743345089
E2F4#1874410.13444825222760.0001818201509632970.00220265801490034
EGR1#195854.988179094810140.0003237398000590710.00330444301977808
EP300#203345.419153380978560.00209386927943890.0121126406156707
FOXA1#3169511.08141974938555.98116883436141e-060.000178731700112123
FOXA2#3170314.77827825159910.0006289192851194480.00517316698579113
HMGN3#932446.542838178680470.00100801277768350.00721858519531591
HNF4G#3174211.50136901057870.01127438304921050.0413704339567315
NR2C2#7182213.04584436209630.00883636412768260.0335439456648387
NR3C1#2908411.97841866493849.4122920812787e-050.00136491304176155
SUZ12#23512220.04631236442520.003824075654154750.0188726319461425
TAF1#687253.343046285745290.002394600090870310.0135161670480681
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815306237460582



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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