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Coexpression cluster:C4629: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4629_salivary_parotid_submaxillary_Whole_stomach_thyroid_breast
|id=C4629
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.12e-52!115;UBERON:0005743!2.04e-21!86;UBERON:0001017!2.11e-21!82;UBERON:0000073!4.23e-21!94;UBERON:0001016!4.23e-21!94;UBERON:0001049!1.59e-20!57;UBERON:0005068!1.59e-20!57;UBERON:0006241!1.59e-20!57;UBERON:0007135!1.59e-20!57;UBERON:0004111!5.18e-19!241;UBERON:0002616!2.21e-18!59;UBERON:0003080!2.94e-18!42;UBERON:0000955!4.07e-18!69;UBERON:0006238!4.07e-18!69;UBERON:0002780!1.20e-17!41;UBERON:0001890!1.20e-17!41;UBERON:0006240!1.20e-17!41;UBERON:0003075!2.79e-16!86;UBERON:0007284!2.79e-16!86;UBERON:0002346!3.07e-16!90;UBERON:0000025!6.95e-16!194;UBERON:0000477!4.42e-15!286;UBERON:0002020!5.51e-15!34;UBERON:0003528!5.51e-15!34;UBERON:0001893!6.70e-15!34;UBERON:0001869!1.37e-14!32;UBERON:0002791!2.58e-14!33;UBERON:0003056!2.59e-14!61;UBERON:0000924!1.81e-13!173;UBERON:0006601!1.81e-13!173;UBERON:0004121!2.63e-13!169;UBERON:0000033!2.64e-13!123;UBERON:0000153!3.01e-13!129;UBERON:0007811!3.01e-13!129;UBERON:0002619!1.36e-12!22;UBERON:0000956!7.53e-12!25;UBERON:0000203!7.53e-12!25;UBERON:0001950!1.12e-11!20;UBERON:0000922!5.52e-11!612;UBERON:0000468!1.15e-10!659;UBERON:0000483!1.54e-10!309;UBERON:0000119!1.69e-10!312;UBERON:0000481!1.88e-09!347;UBERON:0002050!2.61e-09!605;UBERON:0005423!2.61e-09!605;UBERON:0000923!5.00e-09!604;UBERON:0005291!5.00e-09!604;UBERON:0006598!5.00e-09!604;UBERON:0002532!5.00e-09!604;UBERON:0000480!5.36e-09!626;UBERON:0000467!6.61e-09!625;UBERON:0004921!1.25e-08!129;UBERON:0004185!1.25e-08!129;UBERON:0001007!1.02e-07!155;UBERON:0001555!1.02e-07!155;UBERON:0007026!1.02e-07!155;UBERON:0000064!1.23e-07!219;UBERON:0004119!1.60e-07!169;UBERON:0000925!1.60e-07!169;UBERON:0006595!1.60e-07!169
}}

Latest revision as of 14:16, 17 September 2013


Full id: C4629_salivary_parotid_submaxillary_Whole_stomach_thyroid_breast



Phase1 CAGE Peaks

Hg19::chr6:80341003..80341025,+p2@SH3BGRL2
Hg19::chr6:80341039..80341052,+p1@SH3BGRL2
Hg19::chr6:80411337..80411340,+p6@SH3BGRL2


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 organism9.24e-51114
organ system subdivision4.51e-24223
anatomical cluster9.77e-24373
nervous system8.79e-2189
central nervous system1.03e-2081
neural tube1.25e-2056
neural rod1.25e-2056
future spinal cord1.25e-2056
neural keel1.25e-2056
regional part of nervous system1.43e-1953
regional part of brain1.43e-1953
anatomical conduit4.28e-19240
regional part of forebrain2.98e-1841
forebrain2.98e-1841
anterior neural tube2.98e-1841
future forebrain2.98e-1841
brain7.09e-1868
future brain7.09e-1868
tube1.80e-16192
neural plate1.99e-1682
presumptive neural plate1.99e-1682
neurectoderm2.94e-1686
telencephalon1.91e-1534
brain grey matter2.34e-1534
gray matter2.34e-1534
cerebral hemisphere4.19e-1532
regional part of telencephalon1.21e-1432
pre-chordal neural plate4.88e-1461
regional part of cerebral cortex3.62e-1322
ectoderm-derived structure1.42e-12171
ectoderm1.42e-12171
presumptive ectoderm1.42e-12171
cerebral cortex2.34e-1225
pallium2.34e-1225
neocortex2.60e-1220
embryo8.03e-12592
ecto-epithelium3.74e-11104
multi-cellular organism4.36e-11656
developing anatomical structure3.79e-10581
multi-tissue structure7.77e-10342
embryonic structure1.22e-09564
epithelium1.26e-09306
germ layer1.32e-09560
germ layer / neural crest1.32e-09560
embryonic tissue1.32e-09560
presumptive structure1.32e-09560
germ layer / neural crest derived structure1.32e-09560
epiblast (generic)1.32e-09560
cell layer1.55e-09309
anatomical group6.93e-09625
anatomical system8.38e-09624
subdivision of digestive tract1.98e-08118
structure with developmental contribution from neural crest1.35e-07132
digestive system2.32e-07145
digestive tract2.32e-07145
primitive gut2.32e-07145
endoderm-derived structure6.59e-07160
endoderm6.59e-07160
presumptive endoderm6.59e-07160


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.11.64148
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
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
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
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
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
MA0114.11.35563
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
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.22.07011
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
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
MA0164.13.79952
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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
FOXA2#3170216.42030916844350.004810682352105480.0226001013976674
HNF4A#3172215.42152690863580.005444210486686610.024691154204406
MAFF#23764237.54357099329680.0009344774015560320.0067718488302186
MAFK#7975218.06715542521990.003983674744936810.0191182339254873
RXRA#6256213.38307809275550.007196434429465730.0298391462354681
SIX5#147912211.3911435703060.009873820081429030.0370899505623266



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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