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{{Coexpression_clusters
{
|full_id=C951_CD14_Hepatocyte_liver_small_Monocytederived_substantia_spinal
 

Latest revision as of 11:34, 17 September 2013


Full id: C951_CD14_Hepatocyte_liver_small_Monocytederived_substantia_spinal



Phase1 CAGE Peaks

Hg19::chr5:42800558..42800572,-p@chr5:42800558..42800572
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Hg19::chr5:42800843..42800854,-p@chr5:42800843..42800854
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Hg19::chr5:42800880..42800912,-p@chr5:42800880..42800912
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Hg19::chr5:42801300..42801396,-p@chr5:42801300..42801396
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Hg19::chr5:42804827..42804883,-p@chr5:42804827..42804883
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Hg19::chr5:42807162..42807221,-p2@SEPP1
Hg19::chr5:42808287..42808317,-p5@SEPP1
Hg19::chr5:42808318..42808356,-p6@SEPP1
Hg19::chr5:42811986..42812001,-p1@SEPP1


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 organism1.07e-55114
organ system subdivision9.17e-21223
neural tube3.67e-2056
neural rod3.67e-2056
future spinal cord3.67e-2056
neural keel3.67e-2056
central nervous system1.38e-1781
regional part of nervous system1.51e-1753
regional part of brain1.51e-1753
brain2.93e-1668
future brain2.93e-1668
neurectoderm3.47e-1686
neural plate7.81e-1682
presumptive neural plate7.81e-1682
nervous system2.13e-1589
organ1.55e-14503
anatomical cluster5.64e-14373
regional part of forebrain1.10e-1341
forebrain1.10e-1341
anterior neural tube1.10e-1341
future forebrain1.10e-1341
ecto-epithelium4.23e-13104
brain grey matter2.86e-1134
gray matter2.86e-1134
structure with developmental contribution from neural crest5.06e-11132
telencephalon7.16e-1134
multi-tissue structure1.79e-10342
multi-cellular organism2.93e-10656
neural nucleus1.14e-099
nucleus of brain1.14e-099
regional part of telencephalon1.24e-0932
pre-chordal neural plate1.83e-0961
cerebral hemisphere2.77e-0932
embryo8.97e-09592
ectoderm-derived structure9.82e-09171
ectoderm9.82e-09171
presumptive ectoderm9.82e-09171
embryonic structure1.04e-08564
germ layer1.39e-08560
germ layer / neural crest1.39e-08560
embryonic tissue1.39e-08560
presumptive structure1.39e-08560
germ layer / neural crest derived structure1.39e-08560
epiblast (generic)1.39e-08560
anatomical group1.83e-08625
developing anatomical structure1.96e-08581
anatomical conduit2.31e-08240
anatomical system3.57e-08624
tube6.01e-08192
posterior neural tube6.97e-0815
chordal neural plate6.97e-0815
telencephalic nucleus1.63e-077
gastrointestinal system2.45e-0725
brainstem2.92e-076
epithelium4.46e-07306
intestine4.99e-0717
subdivision of digestive tract7.05e-07118
basal ganglion7.13e-079
nuclear complex of neuraxis7.13e-079
aggregate regional part of brain7.13e-079
collection of basal ganglia7.13e-079
cerebral subcortex7.13e-079
cell layer8.27e-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)
MA0003.10.0149552
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.12.25785
MA0019.11.37405
MA0024.10.766783
MA0025.13.75659
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.11.82437
MA0031.11.69202
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.11.04113
MA0051.10.510444
MA0052.11.86771
MA0055.10.22215
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.432181
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.11.20007
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.931587
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.229733
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.12.35992
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.177438
MA0146.10.0045741
MA0147.10.211483
MA0148.11.11902
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.22.0863
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.12.22353
MA0154.10.062786
MA0155.10.0402662
MA0156.10.288314
MA0157.11.57029
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.23.89582e-07
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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
FOXA2#317038.210154584221750.00467281236756890.0220545847277896
HEY1#2346283.591209816093969.88548321897326e-050.00139235331342731



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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