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{{Coexpression_clusters
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|full_id=C3874_caudate_hippocampus_amygdala_putamen_uterus_thalamus_cervix
|id=C3874
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3874_caudate_hippocampus_amygdala_putamen_uterus_thalamus_cervix



Phase1 CAGE Peaks

Hg19::chr1:154842741..154842772,-p1@KCNN3
Hg19::chr1:154842778..154842790,-p8@KCNN3
Hg19::chr1:154842792..154842816,-p7@KCNN3


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.00e-51114
neural tube9.55e-4156
neural rod9.55e-4156
future spinal cord9.55e-4156
neural keel9.55e-4156
central nervous system5.16e-3981
regional part of nervous system7.15e-3853
regional part of brain7.15e-3853
nervous system1.47e-3489
regional part of forebrain3.66e-3241
forebrain3.66e-3241
anterior neural tube3.66e-3241
future forebrain3.66e-3241
brain1.55e-3068
future brain1.55e-3068
brain grey matter5.13e-2834
gray matter5.13e-2834
telencephalon1.54e-2734
neural plate1.11e-2682
presumptive neural plate1.11e-2682
neurectoderm2.51e-2686
regional part of telencephalon4.71e-2632
cerebral hemisphere1.23e-2532
organ system subdivision1.68e-19223
cerebral cortex4.42e-1925
pallium4.42e-1925
anatomical cluster6.81e-19373
structure with developmental contribution from neural crest8.77e-19132
pre-chordal neural plate2.24e-1861
ecto-epithelium2.87e-18104
regional part of cerebral cortex6.09e-1822
anatomical conduit7.69e-17240
tube2.28e-16192
neocortex4.44e-1620
ectoderm-derived structure2.58e-15171
ectoderm2.58e-15171
presumptive ectoderm2.58e-15171
neural nucleus1.48e-109
nucleus of brain1.48e-109
multi-tissue structure1.74e-10342
basal ganglion2.66e-109
nuclear complex of neuraxis2.66e-109
aggregate regional part of brain2.66e-109
collection of basal ganglia2.66e-109
cerebral subcortex2.66e-109
posterior neural tube1.17e-0915
chordal neural plate1.17e-0915
telencephalic nucleus1.26e-087
embryo4.30e-08592
epithelium5.55e-08306
temporal lobe1.06e-076
cell layer1.18e-07309
segmental subdivision of hindbrain4.36e-0712
hindbrain4.36e-0712
presumptive hindbrain4.36e-0712
embryonic structure8.77e-07564
multi-cellular organism9.60e-07656
germ layer9.81e-07560
germ layer / neural crest9.81e-07560
embryonic tissue9.81e-07560
presumptive structure9.81e-07560
germ layer / neural crest derived structure9.81e-07560
epiblast (generic)9.81e-07560


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
MA0014.10.118426
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
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
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.13.21421
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.07067
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
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
EGR1#195834.988179094810140.008056488137383440.0320733233429972
ELF1#199734.258097958807540.01295179875054610.04624364670296
ETS1#211339.728760922202340.001085840092584840.00762482709806144
FOXA1#3169311.08141974938550.000734755275698670.00581473867081104
HMGN3#932438.178547723350590.001827766942164210.0108732143809916
IRF1#365937.63716375356390.002244692747297240.0128126723416394
NFKB1#479035.488063424193840.006049381815655430.0269673633022553
POU2F2#545239.106124057742520.001324165192682130.00882430376202967
SIX5#147912317.0867153554590.0002004060546325010.00239805315533499
YY1#752834.911170749853860.008441455341808260.0329527231233876
ZEB1#6935316.88843201754390.0002075486917327580.00242815927141005
ZNF143#7702313.50087655222790.0004062804962997170.00389172968476989
ZNF263#1012738.221841637010680.001799043925565870.0109454939148418



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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