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Coexpression cluster:C444: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:23, 17 September 2013


Full id: C444_CD14_trachea_tonsil_tongue_throat_salivary_gall



Phase1 CAGE Peaks

Hg19::chr11:1263090..1263101,+p@chr11:1263090..1263101
+
Hg19::chr11:1267107..1267120,+p4@MUC5B
Hg19::chr11:1267285..1267314,+p14@MUC5B
Hg19::chr11:1283125..1283153,+p@chr11:1283125..1283153
+
Hg19::chr11:1283367..1283377,+p@chr11:1283367..1283377
+
Hg19::chr12:10998477..10998481,-p@chr12:10998477..10998481
-
Hg19::chr18:108531..108547,+p@chr18:108531..108547
+
Hg19::chr20:31611261..31611291,+p1@BPIFB6
Hg19::chr20:31611311..31611316,+p11@BPIFB6
Hg19::chr20:31611317..31611336,+p2@BPIFB6
Hg19::chr20:31611463..31611474,+p3@BPIFB6
Hg19::chr20:31830997..31831004,+p@chr20:31830997..31831004
+
Hg19::chr20:31894723..31894752,+p@chr20:31894723..31894752
+
Hg19::chr20:31897591..31897596,+p@chr20:31897591..31897596
+
Hg19::chr20:31897621..31897629,+p@chr20:31897621..31897629
+
Hg19::chr20:31897630..31897644,+p@chr20:31897630..31897644
+
Hg19::chr22:50643240..50643252,+p@chr22:50643240..50643252
+
Hg19::chr9:138415783..138415790,+p@chr9:138415783..138415790
+
Hg19::chr9:138418185..138418192,+p@chr9:138418185..138418192
+
Hg19::chr9:138418232..138418239,+p@chr9:138418232..138418239
+
Hg19::chr9:138418242..138418256,+p@chr9:138418242..138418256
+
Hg19::chr9:138418258..138418269,+p@chr9:138418258..138418269
+


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:0005201extracellular matrix structural constituent0.0217237725185447
GO:0030414protease inhibitor activity0.023489932885906
GO:0004857enzyme inhibitor activity0.0236076769103968
GO:0007155cell adhesion0.033910279053338
GO:0022610biological adhesion0.033910279053338



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
open tracheal system trachea2.34e-792
tonsil2.21e-401
mucosa-associated lymphoid tissue2.21e-401
lymphoid tissue2.21e-401
tonsillar ring2.21e-401
trachea1.28e-237
respiratory airway1.28e-237
throat6.96e-212
tracheobronchial tree1.27e-1115
lower respiratory tract1.27e-1115
segment of respiratory tract2.16e-0847
respiratory tract2.12e-0754


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)
MA0003.10.00288689
MA0004.10.478761
MA0006.10.0694838
MA0007.12.03949
MA0009.10.526253
MA0014.10.0223655
MA0017.10.297619
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.0770177
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.10.170492
MA0042.10.457543
MA0043.10.526535
MA0046.10.516541
MA0048.10.337055
MA0050.10.150446
MA0051.10.22589
MA0052.10.459414
MA0055.10.0249719
MA0056.10
MA0057.12.12634
MA0058.10.333443
MA0059.10.678862
MA0060.10.0258987
MA0061.10.0847828
MA0063.10
MA0066.14.3891
MA0067.10.820123
MA0068.10.0112936
MA0069.10.51311
MA0070.10.503171
MA0071.11.73321
MA0072.10.499187
MA0073.16.69628
MA0074.10.639966
MA0076.10.110503
MA0077.10.49237
MA0078.10.30111
MA0081.10.331815
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.848393
MA0089.10
MA0090.10.118716
MA0091.10.160096
MA0092.10.136418
MA0093.10.530993
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.0724124
MA0103.10.501795
MA0105.10.447321
MA0106.10.259598
MA0107.10.162095
MA0108.20.383574
MA0109.10
MA0111.10.794681
MA0113.10.272101
MA0114.10.15638
MA0115.10.747865
MA0116.10.672581
MA0117.10.560027
MA0119.10.0925355
MA0122.10.583485
MA0124.11.6886
MA0125.10.631059
MA0130.10
MA0131.10.846727
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.660517
MA0139.10.0745458
MA0140.10.199454
MA0141.12.24392
MA0142.10.359701
MA0143.10.74864
MA0144.10.140794
MA0145.10.699444
MA0146.10.358703
MA0147.10.385197
MA0148.10.174705
MA0149.10.192747
MA0062.20.080288
MA0035.20.198962
MA0039.20.204949
MA0138.21.48116
MA0002.22.98442
MA0137.20.578057
MA0104.20.108753
MA0047.20.250458
MA0112.22.19584
MA0065.24.72246
MA0150.10.115337
MA0151.10
MA0152.10.589582
MA0153.10.615584
MA0154.10.142088
MA0155.10.26573
MA0156.10.277694
MA0157.10.337287
MA0158.10
MA0159.10.386598
MA0160.10.18494
MA0161.10
MA0162.10.0975101
MA0163.10.472083
MA0164.10.28168
MA0080.20.248589
MA0018.20.722038
MA0099.20.204301
MA0079.20.188461
MA0102.21.03595
MA0258.13.37568
MA0259.10.713194
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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