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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:31, 17 September 2013


Full id: C802_acute_Whole_chronic_blood_leukemia_Neutrophils_CD34



Phase1 CAGE Peaks

Hg19::chr11:58777262..58777273,-p@chr11:58777262..58777273
-
Hg19::chr12:54691726..54691738,-p9@NFE2
Hg19::chr12:54694738..54694749,-p5@NFE2
Hg19::chr12:54694758..54694805,-p1@NFE2
Hg19::chr17:42466864..42466880,-p1@ITGA2B
Hg19::chr17:4835555..4835578,+p1@GP1BA
Hg19::chr17:4835580..4835593,+p2@GP1BA
Hg19::chr19:41856835..41856871,+p5@TMEM91
Hg19::chr1:207669613..207669634,+p3@CR1
Hg19::chr1:43803475..43803507,+p1@MPL


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

p.valueFDRnGenesnPathwayName
0.0001304200680977750.0275186343686305285ECM-receptor interaction (KEGG):04512
5.62376772811216e-070.00032433580309358388Hematopoietic cell lineage (KEGG):04640
1.02475767170167e-060.000324335803093584466Hemostasis (Reactome):REACT_604



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:0005887integral to plasma membrane0.000837617965512083
GO:0031226intrinsic to plasma membrane0.000837617965512083
GO:0007599hemostasis0.00259404803956199
GO:0044459plasma membrane part0.00259404803956199
GO:0050878regulation of body fluid levels0.00259404803956199
GO:0001850complement component C3a binding0.00259404803956199
GO:0001847opsonin receptor activity0.00259404803956199
GO:0004877complement component C3b receptor activity0.00259404803956199
GO:0004872receptor activity0.00495057300884679
GO:0001846opsonin binding0.00565907477652354
GO:0004875complement receptor activity0.00565907477652354
GO:0004871signal transducer activity0.00691583255524218
GO:0060089molecular transducer activity0.00691583255524218
GO:0005886plasma membrane0.00691583255524218
GO:0015057thrombin receptor activity0.00691583255524218
GO:0001848complement binding0.00777985356856844
GO:0042730fibrinolysis0.0109813829112646
GO:0009611response to wounding0.0118187531185448
GO:0030195negative regulation of blood coagulation0.0129256302981561
GO:0030193regulation of blood coagulation0.0129256302981561
GO:0004888transmembrane receptor activity0.0129256302981561
GO:0050819negative regulation of coagulation0.0141376950497417
GO:0050818regulation of coagulation0.0144236976063516
GO:0007166cell surface receptor linked signal transduction0.0188347888949068
GO:0009605response to external stimulus0.0188347888949068
GO:0030168platelet activation0.0199260400666217
GO:0006958complement activation, classical pathway0.0214868077403124
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0221967666025441
GO:0047485protein N-terminus binding0.0260494934018146
GO:0006956complement activation0.0260494934018146
GO:0002541activation of plasma proteins during acute inflammatory response0.0260494934018146
GO:0016021integral to membrane0.0277034621720535
GO:0031224intrinsic to membrane0.0277034621720535
GO:0065008regulation of biological quality0.0283128582772092
GO:0016064immunoglobulin mediated immune response0.0283128582772092
GO:0022610biological adhesion0.0283128582772092
GO:0007155cell adhesion0.0283128582772092
GO:0019724B cell mediated immunity0.0283128582772092
GO:0008305integrin complex0.0291732855349702
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0335055842626108
GO:0002253activation of immune response0.0335055842626108
GO:0002449lymphocyte mediated immunity0.0335055842626108
GO:0044425membrane part0.0335055842626108
GO:0006959humoral immune response0.0335055842626108
GO:0002250adaptive immune response0.0335055842626108
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0335055842626108
GO:0002443leukocyte mediated immunity0.0335055842626108
GO:0002526acute inflammatory response0.0335055842626108
GO:0032501multicellular organismal process0.0335055842626108
GO:0006950response to stress0.0335055842626108
GO:0050778positive regulation of immune response0.0335055842626108
GO:0007229integrin-mediated signaling pathway0.0335055842626108
GO:0002684positive regulation of immune system process0.0335055842626108
GO:0050776regulation of immune response0.036842459775197
GO:0002682regulation of immune system process0.036842459775197
GO:0007596blood coagulation0.036842459775197
GO:0050817coagulation0.0369156757555923
GO:0051240positive regulation of multicellular organismal process0.0373396381210043
GO:0043235receptor complex0.0378026624244675
GO:0002252immune effector process0.0378026624244675
GO:0045087innate immune response0.0385259798368652
GO:0042060wound healing0.0435130214904965
GO:0005515protein binding0.0435130214904965
GO:0001653peptide receptor activity0.0468444005596366
GO:0008528peptide receptor activity, G-protein coupled0.0468444005596366
GO:0008015blood circulation0.0490961773108645
GO:0003013circulatory system process0.0490961773108645



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>

Cell Type
Ontology termp-valuen
myeloid cell5.86e-48108
common myeloid progenitor5.86e-48108
hematopoietic stem cell9.20e-33168
angioblastic mesenchymal cell9.20e-33168
myeloid leukocyte1.29e-3172
hematopoietic cell4.59e-30177
hematopoietic oligopotent progenitor cell1.50e-29161
hematopoietic multipotent progenitor cell1.50e-29161
myeloid lineage restricted progenitor cell8.47e-2666
classical monocyte1.12e-2442
CD14-positive, CD16-negative classical monocyte1.12e-2442
granulocyte monocyte progenitor cell8.44e-2267
monopoietic cell1.55e-2159
monocyte1.55e-2159
monoblast1.55e-2159
promonocyte1.55e-2159
macrophage dendritic cell progenitor1.61e-2061
defensive cell1.65e-2048
phagocyte1.65e-2048
leukocyte2.18e-16136
hematopoietic lineage restricted progenitor cell6.77e-12120
granulocyte1.88e-118
nongranular leukocyte2.23e-11115
blood cell6.24e-0811
stuff accumulating cell7.70e-0887
neutrophil7.60e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.86e-3598
blood island1.86e-3598
hemolymphoid system1.25e-33108
immune system7.19e-2193
bone marrow1.83e-1976
blood1.67e-1715
haemolymphatic fluid1.67e-1715
organism substance1.67e-1715
bone element2.81e-1782
skeletal element7.75e-1590
lateral plate mesoderm9.65e-13203
skeletal system2.30e-12100
adult organism6.57e-10114
Disease
Ontology termp-valuen
myeloid leukemia5.62e-1531
leukemia7.96e-1139
chronic leukemia1.57e-078
hematologic cancer3.85e-0751
immune system cancer3.85e-0751


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)
MA0003.10.839169
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.0679667
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.963243
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.11.19169
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.631708
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.311193
MA0074.10.4723
MA0076.10.828432
MA0077.10.790956
MA0078.11.39444
MA0081.11.44489
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.857892
MA0091.10.995927
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.741916
MA0106.10.516528
MA0107.11.60878
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.11.31824
MA0114.10.998594
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.11.95291
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.0359093
MA0146.10.243477
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.740103
MA0035.20.437071
MA0039.20.936681
MA0138.20.569505
MA0002.20.80943
MA0137.20.710884
MA0104.20.428616
MA0047.20.504873
MA0112.20.573053
MA0065.20.615279
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.185581
MA0155.11.25014
MA0156.12.0352
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.229496
MA0163.11.30834
MA0164.10.544294
MA0080.21.24809
MA0018.20.517858
MA0099.20.444294
MA0079.21.20328
MA0102.21.36707
MA0258.10.472117
MA0259.10.191914
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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