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{{Coexpression_clusters
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|full_id=C1706_pineal_occipital_paracentral_postcentral_alveolar_parietal_medial
|id=C1706
}}

Latest revision as of 11:50, 17 September 2013


Full id: C1706_pineal_occipital_paracentral_postcentral_alveolar_parietal_medial



Phase1 CAGE Peaks

Hg19::chr13:36429731..36429762,-p4@DCLK1
Hg19::chr13:36429763..36429778,-p7@DCLK1
Hg19::chr13:36429819..36429826,-p12@DCLK1
Hg19::chr13:36429874..36429881,-p13@DCLK1
Hg19::chr19:12945329..12945340,-p5@RTBDN


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
embryonic stem cell6.24e-115
Uber Anatomy
Ontology termp-valuen
central nervous system1.32e-7681
neural tube1.29e-7056
neural rod1.29e-7056
future spinal cord1.29e-7056
neural keel1.29e-7056
nervous system8.90e-7089
regional part of nervous system1.91e-6553
regional part of brain1.91e-6553
brain4.56e-6368
future brain4.56e-6368
regional part of forebrain9.04e-5741
forebrain9.04e-5741
anterior neural tube9.04e-5741
future forebrain9.04e-5741
brain grey matter2.66e-4734
gray matter2.66e-4734
telencephalon5.29e-4734
neural plate6.12e-4682
presumptive neural plate6.12e-4682
adult organism1.55e-44114
cerebral hemisphere9.16e-4432
regional part of telencephalon2.55e-4332
neurectoderm3.69e-4386
pre-chordal neural plate8.30e-3761
regional part of cerebral cortex2.41e-3522
ecto-epithelium2.66e-33104
neocortex1.49e-3120
organ system subdivision3.03e-31223
ectoderm-derived structure4.88e-31171
ectoderm4.88e-31171
presumptive ectoderm4.88e-31171
cerebral cortex1.60e-3025
pallium1.60e-3025
structure with developmental contribution from neural crest5.68e-26132
neural nucleus1.15e-189
nucleus of brain1.15e-189
basal ganglion2.02e-189
nuclear complex of neuraxis2.02e-189
aggregate regional part of brain2.02e-189
collection of basal ganglia2.02e-189
cerebral subcortex2.02e-189
tube4.02e-17192
anatomical cluster3.18e-15373
posterior neural tube1.16e-1415
chordal neural plate1.16e-1415
telencephalic nucleus1.16e-147
gyrus5.39e-146
anatomical conduit1.26e-13240
brainstem6.33e-136
limbic system2.58e-115
parietal lobe2.80e-115
diencephalon6.31e-117
future diencephalon6.31e-117
segmental subdivision of hindbrain3.45e-1012
hindbrain3.45e-1012
presumptive hindbrain3.45e-1012
corpus striatum7.17e-104
striatum7.17e-104
ventral part of telencephalon7.17e-104
future corpus striatum7.17e-104
segmental subdivision of nervous system2.77e-0913
organ part9.74e-09218
multi-cellular organism4.75e-08656
occipital lobe4.78e-085
temporal lobe5.11e-086
caudate-putamen8.85e-083
dorsal striatum8.85e-083
frontal cortex9.04e-083
embryo1.75e-07592
pons2.07e-073
medulla oblongata3.59e-073
myelencephalon3.59e-073
future myelencephalon3.59e-073
epithelium3.77e-07306
cell layer5.86e-07309


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)
MA0003.10.280184
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.98392
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.49156
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
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
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
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.27.06674
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.11.05321
MA0164.10.810347
MA0080.20.456437
MA0018.21.83842
MA0099.21.66926
MA0079.20.00732454
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
CTBP2#1488450.17360027146253.18412825898083e-071.59571579289683e-05
CTCF#1066444.288205098460020.005152015588243280.0239281076186481
EP300#203345.419153380978560.00209386927943890.0121139825878196
FOS#235347.198364247115530.0006947858453382510.00559552274069105
JUN#3725410.01026335386910.0001908531347801070.00230460290707591
JUND#372745.595731153496820.001849593301755460.0109314512388681
NANOG#79923423.39582278481016.64263001833934e-060.000194436557310914
SP1#666744.558705102512720.00407573565781680.0194794872948347
STAT3#677448.415571997723390.0003771527211598630.0037421103026045
TCF7L2#693448.616141250509880.0003438969725982450.0034728539858043
TFAP2A#7020413.2149074984366.38708543065286e-050.00104130629923814
TFAP2C#7022510.80922860986026.77323239348459e-060.000197099364152448



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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