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Coexpression cluster:C2221: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2221_Mesenchymal_Fibroblast_Keratocytes_Keratinocyte_Osteoblast_mesenchymal_Hepatocyte
|id=C2221
}}

Latest revision as of 12:01, 17 September 2013


Full id: C2221_Mesenchymal_Fibroblast_Keratocytes_Keratinocyte_Osteoblast_mesenchymal_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr12:57623876..57623891,+p5@SHMT2
Hg19::chr12:57623907..57623961,+p2@SHMT2
Hg19::chr12:57623963..57623989,+p4@SHMT2
Hg19::chr12:57623992..57624003,+p9@SHMT2


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
animal cell1.09e-30679
eukaryotic cell1.09e-30679
somatic cell2.49e-19588
native cell2.07e-17722
fibroblast7.41e-1576
embryonic cell9.83e-15250
mesodermal cell9.56e-13121
epithelial cell8.95e-11253
non-terminally differentiated cell6.28e-09106
smooth muscle cell6.59e-0943
smooth muscle myoblast6.59e-0943
contractile cell7.20e-0959
muscle precursor cell8.95e-0958
myoblast8.95e-0958
multi-potent skeletal muscle stem cell8.95e-0958
vascular associated smooth muscle cell1.15e-0832
muscle cell1.18e-0855
Uber Anatomy
Ontology termp-valuen
epithelial tube7.31e-13117
unilaminar epithelium5.45e-12148
splanchnic layer of lateral plate mesoderm6.97e-1283
epithelial tube open at both ends2.83e-1159
blood vessel2.83e-1159
blood vasculature2.83e-1159
vascular cord2.83e-1159
vessel3.90e-1168
artery4.11e-1142
arterial blood vessel4.11e-1142
arterial system4.11e-1142
vasculature8.82e-1178
vascular system8.82e-1178
trunk9.60e-11199
organism subdivision4.88e-10264
systemic artery1.85e-0833
systemic arterial system1.85e-0833
trunk mesenchyme8.91e-08122
multilaminar epithelium2.80e-0783
cardiovascular system4.13e-07109
somite5.39e-0771
presomitic mesoderm5.39e-0771
presumptive segmental plate5.39e-0771
dermomyotome5.39e-0771
trunk paraxial mesoderm5.39e-0771
dense mesenchyme tissue6.24e-0773
epithelial vesicle6.60e-0778
skeletal muscle tissue8.65e-0762
striated muscle tissue8.65e-0762
myotome8.65e-0762


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
MA0004.16.93647
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.12.50688
MA0059.11.47051
MA0060.11.01899
MA0061.19.20115
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.14.77747
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.19.86257
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.13.36866
MA0103.10.521546
MA0105.14.42006
MA0106.10.869173
MA0107.17.6741
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
MA0131.13.57792
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
MA0146.10.8309
MA0147.15.25242
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.25.8901
MA0047.20.856092
MA0112.21.65877
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.11.84959
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
MA0162.10.0928415
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0021048
MA0102.21.75932
MA0258.11.88931
MA0259.13.06353
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
ATF3#467422.46317452600873.92475754624726e-060.000127178949231312
CEBPB#105147.971147625824820.0002476385788090830.00267651097301478
E2F1#186944.907389214879320.001724022357361790.0106315051358354
E2F6#187645.017155731697390.00157802193473060.00995512128307635
HEY1#2346244.040111043105710.00375304636917980.0185650741131421
JUND#372746.994663941871030.000417684217818580.00391058019047554
MAX#414946.452555509007120.0005767613195645490.00484721778820326
MXI1#460149.96157162875930.0001015224754950450.00142168219606154
MYC#460945.22228187160940.001344309395272740.00886185248582272
NFKB1#479045.488063424193840.001102199566301980.00766957295656022
SIN3A#2594245.408884726815140.001168172384885160.0079480622609134
TAF1#687243.343046285745290.008005664898701650.0321454685257786
TBP#690843.706770687096390.005296377814784350.0243634779157092
TFAP2A#7020416.5186343730451.34240829060362e-050.000326121841038268
TFAP2C#7022410.80922860986027.32289634782688e-050.00114404782598458
USF1#739146.361499277207960.0006105011399140830.00507159788032826
USF2#7392412.99219738506963.50833029870167e-050.000680294296446535
ZBTB7A#5134147.35190930787590.000342223540015990.00346097456141473



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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