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Coexpression cluster:C1837: Difference between revisions

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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:53, 17 September 2013


Full id: C1837_Neutrophils_Eosinophils_tongue_CD14_esophagus_Whole_blood



Phase1 CAGE Peaks

Hg19::chr1:153330322..153330336,+p1@S100A9
Hg19::chr1:153333121..153333180,+p@chr1:153333121..153333180
+
Hg19::chr1:153333155..153333181,-p@chr1:153333155..153333181
-
Hg19::chr1:153333296..153333313,+p@chr1:153333296..153333313
+
Hg19::chr1:153363539..153363557,-p1@S100A8


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:0045113regulation of integrin biosynthetic process0.0014624853885336
GO:0045112integrin biosynthetic process0.0014624853885336
GO:0006954inflammatory response0.0014624853885336
GO:0009611response to wounding0.00232014234594365
GO:0005615extracellular space0.00289331912031146
GO:0006952defense response0.00295020337246601
GO:0009605response to external stimulus0.00297128665174546
GO:0031532actin cytoskeleton reorganization0.00353195680305831
GO:0044421extracellular region part0.00459120590743029
GO:0007009plasma membrane organization and biogenesis0.00459120590743029
GO:0006950response to stress0.0067680891531925
GO:0030595leukocyte chemotaxis0.0067680891531925
GO:0050900leukocyte migration0.00788879814578809
GO:0005509calcium ion binding0.00788879814578809
GO:0051128regulation of cellular component organization and biogenesis0.0235144913412218
GO:0042330taxis0.0298578589896392
GO:0006935chemotaxis0.0298578589896392
GO:0007626locomotory behavior0.0341155999948796
GO:0006417regulation of translation0.0341155999948796
GO:0031326regulation of cellular biosynthetic process0.0350441653430559
GO:0009889regulation of biosynthetic process0.0363846053814271
GO:0016477cell migration0.0372827430407898
GO:0030036actin cytoskeleton organization and biogenesis0.0377967039412606
GO:0030029actin filament-based process0.0381209320173468
GO:0016044membrane organization and biogenesis0.0397701443440885
GO:0007610behavior0.0397701443440885
GO:0051674localization of cell0.0480454413454034
GO:0006928cell motility0.0480454413454034



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
myeloid leukocyte6.34e-5172
defensive cell1.23e-4848
phagocyte1.23e-4848
monopoietic cell3.99e-4859
monocyte3.99e-4859
monoblast3.99e-4859
promonocyte3.99e-4859
macrophage dendritic cell progenitor7.78e-4661
classical monocyte2.66e-4342
CD14-positive, CD16-negative classical monocyte2.66e-4342
myeloid lineage restricted progenitor cell9.94e-4166
granulocyte monocyte progenitor cell8.41e-4067
myeloid cell1.48e-34108
common myeloid progenitor1.48e-34108
leukocyte7.23e-28136
nongranular leukocyte3.73e-26115
hematopoietic stem cell2.24e-24168
angioblastic mesenchymal cell2.24e-24168
hematopoietic oligopotent progenitor cell4.22e-22161
hematopoietic multipotent progenitor cell4.22e-22161
hematopoietic cell1.02e-21177
stuff accumulating cell3.67e-2187
hematopoietic lineage restricted progenitor cell5.75e-21120
granulocyte1.87e-098
intermediate monocyte1.17e-089
CD14-positive, CD16-positive monocyte1.17e-089
endo-epithelial cell2.40e-0842
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.22e-4398
blood island4.22e-4398
hemolymphoid system1.67e-39108
bone marrow5.93e-3476
immune system9.41e-3193
bone element6.34e-3082
skeletal element7.39e-2990
skeletal system7.64e-24100
lateral plate mesoderm5.83e-14203
blood1.16e-0915
haemolymphatic fluid1.16e-0915
organism substance1.16e-0915
musculoskeletal system7.15e-08167
adult organism1.87e-07114
embryonic structure5.28e-07564
mesoderm8.34e-07315
mesoderm-derived structure8.34e-07315
presumptive mesoderm8.34e-07315


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)
MA0003.10.280184
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.12.58312
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.22.16859
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.868598
MA0146.11.82062
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.21.50443
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.25.90885
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0850863
MA0102.21.66336
MA0258.12.47453
MA0259.10.395396
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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