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Coexpression cluster:C1028: Difference between revisions

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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:36, 17 September 2013


Full id: C1028_Alveolar_Renal_iPS_teratocarcinoma_H9_HES3GFP_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr14:104033742..104033743,+p1@ENST00000364314
Hg19::chr16:3064836..3064855,+p@chr16:3064836..3064855
+
Hg19::chr16:3068178..3068191,-p1@CLDN6
Hg19::chr16:3068393..3068407,+p@chr16:3068393..3068407
+
Hg19::chr19:18557270..18557282,-p2@ELL
Hg19::chr22:47030082..47030087,+p@chr22:47030082..47030087
+
Hg19::chr2:234322838..234322854,+p@chr2:234322838..234322854
+
Hg19::chr4:25679305..25679316,+p@chr4:25679305..25679316
+


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:0008159positive transcription elongation factor activity0.0152784505458963
GO:0006368RNA elongation from RNA polymerase II promoter0.0152784505458963
GO:0003711transcription elongation regulator activity0.0152784505458963
GO:0006354RNA elongation0.0152784505458963
GO:0016338calcium-independent cell-cell adhesion0.0152784505458963
GO:0016607nuclear speck0.0374541676159651
GO:0005923tight junction0.0374541676159651
GO:0043296apical junction complex0.0374541676159651
GO:0016327apicolateral plasma membrane0.0374541676159651
GO:0016604nuclear body0.0374541676159651



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
nephron tubule epithelium6.55e-1710
nephron epithelium5.34e-1615
renal tubule5.34e-1615
nephron tubule5.34e-1615
nephron5.34e-1615
uriniferous tubule5.34e-1615
nephrogenic mesenchyme5.34e-1615
excretory tube5.75e-1516
kidney epithelium5.75e-1516
cortex of kidney3.40e-1412
renal parenchyma3.40e-1412
kidney5.76e-1226
kidney mesenchyme5.76e-1226
upper urinary tract5.76e-1226
kidney rudiment5.76e-1226
kidney field5.76e-1226
cortex2.58e-1115
parenchyma2.58e-1115
renal cortex tubule3.82e-103
region of nephron tubule3.82e-103
proximal tubule3.82e-103
cavitated compound organ6.72e-1031
ciliary epithelium1.40e-093
ciliary body1.40e-093
lower lobe of right lung4.11e-081
right lung lobe4.11e-081
lower lobe of lung4.11e-081
lobe of lung4.11e-081
right lung4.11e-081
trunk region element1.92e-07101
atypical epithelium2.14e-074


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)
MA0003.10.140538
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.118169
MA0056.10
MA0057.10.632427
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.215282
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.11.01596
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.792149
MA0105.10.279181
MA0106.10.59853
MA0107.11.23931
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.11.25866
MA0146.11.26525
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.22.21238
MA0039.20.0325944
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.458158
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.10.43752
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.194027
MA0163.10.141536
MA0164.10.627336
MA0080.21.48508
MA0018.21.46097
MA0099.20.523145
MA0079.20.481761
MA0102.21.46209
MA0258.10.209744
MA0259.10.699589
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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