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Coexpression cluster:C2103: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2103_Fibroblast_putamen_left_caudate_hippocampus_heart_amniotic
|id=C2103
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2103_Fibroblast_putamen_left_caudate_hippocampus_heart_amniotic



Phase1 CAGE Peaks

Hg19::chr11:12030131..12030183,-p1@DKK3
Hg19::chr11:12030588..12030599,-p9@DKK3
Hg19::chr11:12030633..12030644,-p8@DKK3
Hg19::chr11:12030834..12030845,-p7@DKK3


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 cell1.27e-10250
mesodermal cell1.55e-07121
fibroblast2.42e-0776
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.43e-33171
ectoderm1.43e-33171
presumptive ectoderm1.43e-33171
structure with developmental contribution from neural crest2.44e-32132
anatomical cluster1.18e-31373
ecto-epithelium6.71e-30104
neural plate4.17e-2982
presumptive neural plate4.17e-2982
epithelium4.56e-29306
cell layer6.29e-29309
anatomical conduit6.27e-28240
neural tube6.69e-2756
neural rod6.69e-2756
future spinal cord6.69e-2756
neural keel6.69e-2756
brain1.54e-2668
future brain1.54e-2668
central nervous system3.68e-2681
neurectoderm4.43e-2686
regional part of nervous system4.28e-2553
regional part of brain4.28e-2553
anatomical system1.93e-23624
tube2.56e-23192
multi-tissue structure2.79e-23342
anatomical group4.04e-23625
nervous system6.43e-2389
multi-cellular organism6.83e-23656
organ part1.66e-19218
pre-chordal neural plate3.03e-1961
regional part of forebrain1.71e-1841
forebrain1.71e-1841
anterior neural tube1.71e-1841
future forebrain1.71e-1841
brain grey matter1.00e-1734
gray matter1.00e-1734
telencephalon1.66e-1734
cerebral hemisphere7.46e-1732
regional part of telencephalon1.17e-1632
embryonic structure3.49e-14564
developing anatomical structure6.03e-14581
organ1.52e-13503
embryo1.85e-13592
germ layer3.64e-13560
germ layer / neural crest3.64e-13560
embryonic tissue3.64e-13560
presumptive structure3.64e-13560
germ layer / neural crest derived structure3.64e-13560
epiblast (generic)3.64e-13560
organ system subdivision6.81e-13223
cerebral cortex6.97e-1325
pallium6.97e-1325
adult organism7.98e-13114
regional part of cerebral cortex1.80e-1122
splanchnic layer of lateral plate mesoderm5.37e-1183
vasculature5.88e-1178
vascular system5.88e-1178
neocortex3.01e-1020
posterior neural tube1.14e-0915
chordal neural plate1.14e-0915
vessel7.45e-0968
epithelial tube open at both ends1.95e-0859
blood vessel1.95e-0859
blood vasculature1.95e-0859
vascular cord1.95e-0859
surface structure3.18e-0899
circulatory system3.22e-08112
organ component layer5.38e-0866
segmental subdivision of hindbrain6.07e-0812
hindbrain6.07e-0812
presumptive hindbrain6.07e-0812
extraembryonic membrane2.09e-0714
membranous layer2.09e-0714
head2.10e-0756
segmental subdivision of nervous system2.75e-0713
cardiovascular system3.22e-07109
epithelial tube4.63e-07117


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)
MA0003.14.10305
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.16.06873
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.11.92841
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.19.02144
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.27.89088
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.23.12566
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.15.0369
MA0163.14.57046
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.211.2591
MA0102.21.75932
MA0258.11.88931
MA0259.10.471671
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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