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Coexpression cluster:C620: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0029051532235098

Latest revision as of 11:27, 17 September 2013


Full id: C620_CD14_Smooth_Fibroblast_Mast_signet_normal_meningioma



Phase1 CAGE Peaks

Hg19::chr11:35160709..35160726,+p1@CD44
Hg19::chr11:35198186..35198209,+p7@CD44
Hg19::chr11:35198211..35198235,+p11@CD44
Hg19::chr11:35198243..35198260,+p18@CD44
Hg19::chr11:35201826..35201855,+p3@CD44
Hg19::chr11:35201856..35201865,+p15@CD44
Hg19::chr11:35201889..35201914,+p2@CD44
Hg19::chr11:35211386..35211412,+p10@CD44
Hg19::chr11:35211437..35211460,+p8@CD44
Hg19::chr11:35211511..35211550,+p5@CD44
Hg19::chr11:35236421..35236435,+p6@CD44
Hg19::chr11:35251132..35251143,+p17@CD44
Hg19::chr11:35252320..35252338,+p13@CD44
Hg19::chr11:35253300..35253312,+p@chr11:35253300..35253312
+


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
defensive cell6.83e-2148
phagocyte6.83e-2148
granulocyte monocyte progenitor cell2.06e-1967
classical monocyte2.57e-1942
CD14-positive, CD16-negative classical monocyte2.57e-1942
myeloid leukocyte4.97e-1972
myeloid lineage restricted progenitor cell3.96e-1866
macrophage dendritic cell progenitor4.41e-1861
monopoietic cell1.66e-1759
monocyte1.66e-1759
monoblast1.66e-1759
promonocyte1.66e-1759
somatic cell1.35e-14588
stuff accumulating cell8.64e-1387
multi fate stem cell4.48e-12427
somatic stem cell4.61e-12433
native cell6.26e-11722
stem cell1.84e-10441
animal cell1.05e-09679
eukaryotic cell1.05e-09679
connective tissue cell1.60e-09361
mesenchymal cell3.39e-09354
motile cell2.85e-08386
hematopoietic lineage restricted progenitor cell5.21e-08120
myeloid cell9.84e-08108
common myeloid progenitor9.84e-08108
leukocyte2.69e-07136
nongranular leukocyte5.55e-07115
Uber Anatomy
Ontology termp-valuen
musculoskeletal system7.15e-19167
bone marrow9.90e-1876
skeletal element2.62e-1590
skeletal system1.38e-14100
bone element2.28e-1482
hematopoietic system7.48e-1398
blood island7.48e-1398
immune system1.20e-1193
hemolymphoid system4.13e-10108
surface structure1.61e-0999
mesoderm2.11e-09315
mesoderm-derived structure2.11e-09315
presumptive mesoderm2.11e-09315
connective tissue6.64e-09371
lateral plate mesoderm4.39e-08203
integument2.45e-0746
integumental system2.45e-0746
skin of body7.69e-0741


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)
MA0003.10.000123988
MA0004.12.96183
MA0006.10.152601
MA0007.10.260673
MA0009.14.05033
MA0014.10.000542531
MA0017.10.181071
MA0019.11.04045
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.110534
MA0050.10.265714
MA0051.10.359609
MA0052.11.51148
MA0055.10.00349085
MA0056.10
MA0057.10.0243088
MA0058.11.7263
MA0059.13.22501
MA0060.10.0773489
MA0061.10.841286
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.169955
MA0069.10.681911
MA0070.10.671241
MA0071.10.878639
MA0072.10.666958
MA0073.10.0345424
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.11.13748
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0103438
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.247341
MA0093.14.42008
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.448026
MA0105.10.701161
MA0106.10.399649
MA0107.10.348426
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.548507
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.11.72198
MA0136.10.966693
MA0139.10.0564547
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.11.8739
MA0144.10.0953756
MA0145.10.16253
MA0146.10.148267
MA0147.11.75017
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.000193995
MA0138.20.44894
MA0002.20.0708857
MA0137.20.168782
MA0104.21.42323
MA0047.20.388882
MA0112.20.0554275
MA0065.20.16797
MA0150.10.624926
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.11.01572
MA0155.10.0505475
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.10.00136062
MA0163.10.194919
MA0164.10.425415
MA0080.20.46983
MA0018.21.03559
MA0099.20.333432
MA0079.24.29033e-06
MA0102.21.22472
MA0258.10.089643
MA0259.11.2329
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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