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Coexpression cluster:C4018: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4018_occipital_Osteoblast_brain_Dendritic_Monocytederived_submaxillary_Adipocyte
|id=C4018
}}

Latest revision as of 12:37, 17 September 2013


Full id: C4018_occipital_Osteoblast_brain_Dendritic_Monocytederived_submaxillary_Adipocyte



Phase1 CAGE Peaks

Hg19::chr20:23614485..23614564,-p@chr20:23614485..23614564
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Hg19::chr20:23615923..23615953,-p@chr20:23615923..23615953
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Hg19::chr20:23615955..23616000,-p@chr20:23615955..23616000
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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>

Uber Anatomy
Ontology termp-valuen
adult organism6.17e-27114
multi-cellular organism1.76e-26656
germ layer6.87e-26560
germ layer / neural crest6.87e-26560
embryonic tissue6.87e-26560
presumptive structure6.87e-26560
germ layer / neural crest derived structure6.87e-26560
epiblast (generic)6.87e-26560
embryonic structure7.27e-26564
anatomical system3.92e-25624
anatomical group6.98e-25625
developing anatomical structure9.58e-24581
embryo1.06e-22592
organ1.27e-19503
mesoderm1.02e-18315
mesoderm-derived structure1.02e-18315
presumptive mesoderm1.02e-18315
bone marrow2.08e-1676
musculoskeletal system5.30e-15167
bone element2.29e-1482
skeletal element2.72e-1490
lateral plate mesoderm4.03e-14203
skeletal system8.94e-14100
immune system1.52e-1393
hematopoietic system7.66e-1298
blood island7.66e-1298
hemolymphoid system9.04e-12108
neural tube4.52e-1156
neural rod4.52e-1156
future spinal cord4.52e-1156
neural keel4.52e-1156
regional part of nervous system8.00e-1053
regional part of brain8.00e-1053
anatomical conduit2.04e-09240
tissue2.87e-09773
regional part of forebrain6.16e-0841
forebrain6.16e-0841
anterior neural tube6.16e-0841
future forebrain6.16e-0841
tube8.21e-08192
neural plate1.08e-0782
presumptive neural plate1.08e-0782
structure with developmental contribution from neural crest1.90e-07132
central nervous system3.10e-0781
multi-tissue structure3.60e-07342
brain grey matter3.60e-0734
gray matter3.60e-0734
telencephalon7.49e-0734
brain7.84e-0768
future brain7.84e-0768
regional part of telencephalon9.30e-0732


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)
MA0003.10.708947
MA0004.11.93041
MA0006.10.639288
MA0007.11.88666
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.36698
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.12.37746
MA0081.10.714712
MA0083.12.96495
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.12.19699
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.13.75777
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.12.22591
MA0259.12.40872
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
NR3C1#290829.982015554115360.01278474365547170.046051798393937



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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