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Coexpression cluster:C2349: Difference between revisions

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{{Coexpression_clusters
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regulation of calcium-dependent cell-cell adhesion!0.00259036853879666!53827$GO:0046586!regulation of calcium-dependent cell-cell adhesion!0.00259036853879666!53827$GO:0030033!microvillus biogenesis!0.006475540085248!53827$GO:0032528!microvillus organization and biogenesis!0.006475540085248!53827$GO:0000339!RNA cap binding!0.0072523913889013!10073$GO:0022408!negative regulation of cell-cell adhesion!0.00805738235098189!53827$GO:0045296!cadherin binding!0.00805738235098189!53827$GO:0022407!regulation of cell-cell adhesion!0.00805738235098189!53827$GO:0050839!cell adhesion molecule binding!0.00805738235098189!53827$GO:0016339!calcium-dependent cell-cell adhesion!0.0122408727264318!53827$GO:0007162!negative regulation of cell adhesion!0.0122408727264318!53827$GO:0022892!substrate-specific transporter activity!0.0198064840396804!53827;10073$GO:0030155!regulation of cell adhesion!0.0262770403496228!53827$GO:0005643!nuclear pore!0.0298227869868878!10073$GO:0006606!protein import into nucleus!0.0298227869868878!10073$GO:0046930!pore complex!0.0298227869868878!10073$GO:0051170!nuclear import!0.0298227869868878!10073$GO:0044453!nuclear membrane part!0.0318961541352686!10073$GO:0017038!protein import!0.0332065413839154!10073$GO:0031965!nuclear membrane!0.0341084762377736!10073$GO:0006913!nucleocytoplasmic transport!0.0341084762377736!10073$GO:0008565!protein transporter activity!0.0341084762377736!10073$GO:0051169!nuclear transport!0.0341084762377736!10073$GO:0016043!cellular component organization and biogenesis!0.0341084762377736!53827;10073$GO:0005635!nuclear envelope!0.0376325929129757!10073$GO:0032990!cell part morphogenesis!0.0376325929129757!53827$GO:0048858!cell projection morphogenesis!0.0376325929129757!53827$GO:0030030!cell projection organization and biogenesis!0.0376325929129757!53827$GO:0006605!protein targeting!0.0388204651484896!10073$GO:0006810!transport!0.0413724656089171!53827;10073$GO:0051234!establishment of 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A0047.2;0.856092,MA0112.2;0.187982,MA0065.2;1.09513,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;1.21162,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.918944,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.327251,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2349_Mast_CD14_Smooth_Mesenchymal_Hair_mesothelioma_papillotubular
|id=C2349
}}

Latest revision as of 12:03, 17 September 2013


Full id: C2349_Mast_CD14_Smooth_Mesenchymal_Hair_mesothelioma_papillotubular



Phase1 CAGE Peaks

Hg19::chr15:75913265..75913337,-p4@SNUPN
Hg19::chr16:27258633..27258637,+p@chr16:27258633..27258637
+
Hg19::chr19:35646092..35646138,+p2@FXYD5
Hg19::chr19:35646149..35646177,+p5@FXYD5


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

GO IDGO nameFDR corrected p-value
GO:0046588negative regulation of calcium-dependent cell-cell adhesion0.00259036853879666
GO:0046586regulation of calcium-dependent cell-cell adhesion0.00259036853879666
GO:0030033microvillus biogenesis0.006475540085248
GO:0032528microvillus organization and biogenesis0.006475540085248
GO:0000339RNA cap binding0.0072523913889013
GO:0022408negative regulation of cell-cell adhesion0.00805738235098189
GO:0045296cadherin binding0.00805738235098189
GO:0022407regulation of cell-cell adhesion0.00805738235098189
GO:0050839cell adhesion molecule binding0.00805738235098189
GO:0016339calcium-dependent cell-cell adhesion0.0122408727264318
GO:0007162negative regulation of cell adhesion0.0122408727264318
GO:0022892substrate-specific transporter activity0.0198064840396804
GO:0030155regulation of cell adhesion0.0262770403496228
GO:0005643nuclear pore0.0298227869868878
GO:0006606protein import into nucleus0.0298227869868878
GO:0046930pore complex0.0298227869868878
GO:0051170nuclear import0.0298227869868878
GO:0044453nuclear membrane part0.0318961541352686
GO:0017038protein import0.0332065413839154
GO:0031965nuclear membrane0.0341084762377736
GO:0006913nucleocytoplasmic transport0.0341084762377736
GO:0008565protein transporter activity0.0341084762377736
GO:0051169nuclear transport0.0341084762377736
GO:0016043cellular component organization and biogenesis0.0341084762377736
GO:0005635nuclear envelope0.0376325929129757
GO:0032990cell part morphogenesis0.0376325929129757
GO:0048858cell projection morphogenesis0.0376325929129757
GO:0030030cell projection organization and biogenesis0.0376325929129757
GO:0006605protein targeting0.0388204651484896
GO:0006810transport0.0413724656089171
GO:0051234establishment of localization0.0420472423208777
GO:0051179localization0.047836148453937



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
defensive cell2.17e-2348
phagocyte2.17e-2348
classical monocyte3.99e-2142
CD14-positive, CD16-negative classical monocyte3.99e-2142
somatic cell1.85e-20588
native cell2.07e-20722
myeloid lineage restricted progenitor cell3.07e-2066
granulocyte monocyte progenitor cell4.06e-2067
animal cell9.63e-20679
eukaryotic cell9.63e-20679
monopoietic cell1.40e-1959
monocyte1.40e-1959
monoblast1.40e-1959
promonocyte1.40e-1959
stem cell2.78e-19441
multi fate stem cell3.18e-19427
myeloid leukocyte5.90e-1972
somatic stem cell7.86e-19433
macrophage dendritic cell progenitor1.22e-1861
myeloid cell1.27e-15108
common myeloid progenitor1.27e-15108
mesenchymal cell1.14e-13354
connective tissue cell2.18e-13361
stuff accumulating cell4.92e-1387
vascular associated smooth muscle cell9.28e-1132
motile cell1.11e-09386
smooth muscle cell3.94e-0943
smooth muscle myoblast3.94e-0943
muscle cell1.60e-0855
muscle precursor cell8.45e-0858
myoblast8.45e-0858
multi-potent skeletal muscle stem cell8.45e-0858
contractile cell2.19e-0759
mesodermal cell7.12e-07121
fibroblast9.67e-0776


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
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
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.10.418966
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235336.74846648167080.005032452776317940.0234614916304736
THAP1#55145215.68457230142570.005840469678357920.0262444201332942



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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