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Coexpression cluster:C437: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:23, 17 September 2013


Full id: C437_CD4_CD8_Natural_CD19_thyroid_Peripheral_Mast



Phase1 CAGE Peaks

Hg19::chr18:13744183..13744186,+p@chr18:13744183..13744186
+
Hg19::chr19:54053807..54053810,+p@chr19:54053807..54053810
+
Hg19::chr19:54061420..54061436,+p@chr19:54061420..54061436
+
Hg19::chr19:54061936..54061950,+p@chr19:54061936..54061950
+
Hg19::chr19:54061968..54061982,+p@chr19:54061968..54061982
+
Hg19::chr19:54062000..54062050,+p@chr19:54062000..54062050
+
Hg19::chr19:54062055..54062070,+p@chr19:54062055..54062070
+
Hg19::chr19:54062078..54062093,+p@chr19:54062078..54062093
+
Hg19::chr19:54062149..54062157,+p@chr19:54062149..54062157
+
Hg19::chr19:54062279..54062292,+p@chr19:54062279..54062292
+
Hg19::chr19:54062315..54062327,+p@chr19:54062315..54062327
+
Hg19::chr19:54062365..54062378,+p@chr19:54062365..54062378
+
Hg19::chr19:54062481..54062494,+p@chr19:54062481..54062494
+
Hg19::chr19:54062498..54062552,+p@chr19:54062498..54062552
+
Hg19::chr19:54062603..54062676,+p@chr19:54062603..54062676
+
Hg19::chr19:54062841..54062918,+p@chr19:54062841..54062918
+
Hg19::chr19:54062986..54063018,+p@chr19:54062986..54063018
+
Hg19::chr19:54063091..54063178,+p@chr19:54063091..54063178
+
Hg19::chr19:54063216..54063233,+p@chr19:54063216..54063233
+
Hg19::chr19:54063237..54063327,+p@chr19:54063237..54063327
+
Hg19::chr19:54067349..54067352,+p@chr19:54067349..54067352
+
Hg19::chr19:54078774..54078778,+p@chr19:54078774..54078778
+
Hg19::chr3:99547474..99547482,+p@chr3:99547474..99547482
+


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 organism1.34e-20114
neural tube9.81e-1756
neural rod9.81e-1756
future spinal cord9.81e-1756
neural keel9.81e-1756
regional part of nervous system8.83e-1653
regional part of brain8.83e-1653
regional part of forebrain5.46e-1441
forebrain5.46e-1441
anterior neural tube5.46e-1441
future forebrain5.46e-1441
neurectoderm2.20e-1386
neural plate6.86e-1382
presumptive neural plate6.86e-1382
brain4.53e-1168
future brain4.53e-1168
brain grey matter2.42e-1034
gray matter2.42e-1034
telencephalon4.76e-1034
central nervous system1.05e-0981
regional part of telencephalon4.66e-0932
cerebral hemisphere7.36e-0932
pre-chordal neural plate2.09e-0861
ecto-epithelium5.93e-08104
bone element7.73e-0882
nervous system1.20e-0789
regional part of cerebral cortex2.11e-0722
hematopoietic system2.69e-0798
blood island2.69e-0798
neocortex2.75e-0720
bone marrow5.69e-0776
structure with developmental contribution from neural crest7.59e-07132


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)
MA0003.11.16184e-08
MA0004.10.148499
MA0006.10.0632578
MA0007.10.137043
MA0009.127.1883
MA0014.17.37118e-06
MA0017.10.0812903
MA0019.10.250001
MA0024.10.419164
MA0025.10.630648
MA0027.12.07466
MA0028.10.0703882
MA0029.10.435662
MA0030.10.425859
MA0031.10.371592
MA0038.10.21714
MA0040.10.440685
MA0041.10.483206
MA0042.14.22099
MA0043.10.510506
MA0046.10.500598
MA0048.10.00412155
MA0050.10.14079
MA0051.10.214141
MA0052.10.444013
MA0055.10.000156118
MA0056.10
MA0057.10.00365463
MA0058.10.0939409
MA0059.10.0932742
MA0060.10.0226691
MA0061.10.0163713
MA0063.10
MA0066.11.16636
MA0067.10.802392
MA0068.10.0481509
MA0069.10.497197
MA0070.13.13461
MA0071.10.190167
MA0072.10.483399
MA0073.14.46781e-06
MA0074.10.213609
MA0076.10.102323
MA0077.10.476645
MA0078.10.287843
MA0081.10.0933581
MA0083.10.516887
MA0084.10.981601
MA0087.10.481255
MA0088.10.0642579
MA0089.10
MA0090.10.110205
MA0091.10.15013
MA0092.10.127244
MA0093.10.0645787
MA0095.10
MA0098.10
MA0100.10.227084
MA0101.10.0660267
MA0103.10.469617
MA0105.10.00274777
MA0106.10.247115
MA0107.10.0374129
MA0108.25.68845
MA0109.10
MA0111.10.117802
MA0113.10.259368
MA0114.10.0357353
MA0115.10.730438
MA0116.10.0385791
MA0117.10.543727
MA0119.10.0851434
MA0122.10.567011
MA0124.10.691722
MA0125.10.614264
MA0130.10
MA0131.10.302006
MA0132.10
MA0133.10
MA0135.10.537249
MA0136.10.222179
MA0139.10.0139039
MA0140.10.188358
MA0141.10.092378
MA0142.10.345512
MA0143.10.259501
MA0144.10.0312488
MA0145.10.0794871
MA0146.10.0111242
MA0147.10.0397742
MA0148.10.164295
MA0149.10.18183
MA0062.20.0152768
MA0035.20.18788
MA0039.24.58713e-07
MA0138.20.288795
MA0002.20.0879293
MA0137.20.073361
MA0104.20.022476
MA0047.20.238164
MA0112.20.00106228
MA0065.20.00138326
MA0150.10.347297
MA0151.10
MA0152.10.192836
MA0153.10.598889
MA0154.10.0161135
MA0155.10.000886512
MA0156.10.0744198
MA0157.10.323429
MA0158.10
MA0159.10.0399934
MA0160.10.174237
MA0161.10
MA0162.13.33344e-05
MA0163.19.19378e-06
MA0164.10.268764
MA0080.20.0646165
MA0018.20.248141
MA0099.20.193081
MA0079.20
MA0102.21.01759
MA0258.10.118144
MA0259.10.0427194
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

No analysis results for this cluster

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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