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{{Coexpression_clusters
{
|full_id=C746_Neutrophils_chronic_Monocytederived_CD4_Whole_Hodgkin_lymph
|

Latest revision as of 11:30, 17 September 2013


Full id: C746_Neutrophils_chronic_Monocytederived_CD4_Whole_Hodgkin_lymph



Phase1 CAGE Peaks

Hg19::chr12:15095224..15095238,-p@chr12:15095224..15095238
-
Hg19::chr12:15095377..15095412,-p@chr12:15095377..15095412
-
Hg19::chr12:15095596..15095637,-p@chr12:15095596..15095637
-
Hg19::chr12:15097732..15097776,-p@chr12:15097732..15097776
-
Hg19::chr16:30198754..30198769,+p@chr16:30198754..30198769
+
Hg19::chr22:37621663..37621687,-p4@RAC2
Hg19::chr2:234104079..234104082,+p4@INPP5D
Hg19::chrX:70327539..70327558,-p@chrX:70327539..70327558
-
Hg19::chrX:70327608..70327641,-p@chrX:70327608..70327641
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Hg19::chrX:70327646..70327667,-p@chrX:70327646..70327667
-
Hg19::chrX:70329181..70329194,-p2@IL2RG


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
2.03984814542931e-050.0047782444038979275B cell receptor signaling pathway (KEGG):04662
2.26457080753455e-050.0047782444038979279Fc epsilon RI signaling pathway (KEGG):04664
3.28059829023111e-050.00479055337409632295Fc gamma R-mediated phagocytosis (KEGG):04666
3.78400740449947e-050.004790553374096322102IL-3 Signaling Pathway (Wikipathways):WP286
1.48230348787841e-050.0047782444038979264IL-4 signaling Pathway (Wikipathways):WP395



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:0019982interleukin-7 binding0.0047242008376489
GO:0004917interleukin-7 receptor activity0.0047242008376489
GO:0004913interleukin-4 receptor activity0.0047242008376489
GO:0019979interleukin-4 binding0.0047242008376489
GO:0019976interleukin-2 binding0.0047242008376489
GO:0004911interleukin-2 receptor activity0.0047242008376489
GO:0046030inositol trisphosphate phosphatase activity0.00944701104561127
GO:0004445inositol-polyphosphate 5-phosphatase activity0.00944701104561127
GO:0004907interleukin receptor activity0.0314511171465861
GO:0007165signal transduction0.0314511171465861
GO:0019965interleukin binding0.0314511171465861
GO:0006955immune response0.0314511171465861
GO:0007154cell communication0.0314511171465861
GO:0030031cell projection biogenesis0.0314511171465861
GO:0009897external side of plasma membrane0.0314511171465861
GO:0002376immune system process0.0316296020883855
GO:0004437inositol or phosphatidylinositol phosphatase activity0.0316296020883855
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0361485493485189
GO:0019838growth factor binding0.0441463508053512
GO:0019955cytokine binding0.0466375408730237



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
hematopoietic stem cell6.05e-101168
angioblastic mesenchymal cell6.05e-101168
hematopoietic cell2.55e-97177
hematopoietic oligopotent progenitor cell1.75e-96161
hematopoietic multipotent progenitor cell1.75e-96161
leukocyte4.34e-92136
nongranular leukocyte3.95e-80115
hematopoietic lineage restricted progenitor cell3.83e-79120
myeloid cell2.67e-52108
common myeloid progenitor2.67e-52108
myeloid leukocyte1.96e-4372
granulocyte monocyte progenitor cell4.35e-3967
lymphocyte1.98e-3853
common lymphoid progenitor1.98e-3853
lymphoid lineage restricted progenitor cell8.12e-3852
macrophage dendritic cell progenitor2.46e-3761
myeloid lineage restricted progenitor cell5.07e-3766
nucleate cell2.77e-3655
monopoietic cell3.42e-3659
monocyte3.42e-3659
monoblast3.42e-3659
promonocyte3.42e-3659
defensive cell1.21e-3348
phagocyte1.21e-3348
classical monocyte2.90e-2942
CD14-positive, CD16-negative classical monocyte2.90e-2942
mesenchymal cell6.18e-23354
connective tissue cell1.31e-21361
T cell1.75e-1925
pro-T cell1.75e-1925
motile cell4.94e-17386
lymphocyte of B lineage8.59e-1724
pro-B cell8.59e-1724
mature alpha-beta T cell2.54e-1618
alpha-beta T cell2.54e-1618
immature T cell2.54e-1618
mature T cell2.54e-1618
immature alpha-beta T cell2.54e-1618
multi fate stem cell4.29e-12427
stuff accumulating cell7.40e-1287
somatic stem cell9.90e-12433
stem cell3.17e-11441
B cell9.88e-1114
CD8-positive, alpha-beta T cell2.06e-1011
CD4-positive, alpha-beta T cell8.55e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.26e-5098
blood island1.26e-5098
hemolymphoid system7.40e-46108
immune system1.01e-3493
bone marrow1.70e-3476
bone element2.68e-3082
skeletal element1.27e-2590
skeletal system6.59e-21100
connective tissue8.08e-20371
lateral plate mesoderm2.00e-15203
blood3.36e-1215
haemolymphatic fluid3.36e-1215
organism substance3.36e-1215
Disease
Ontology termp-valuen
hematologic cancer7.56e-1951
immune system cancer7.56e-1951
leukemia2.83e-1539
myeloid leukemia1.45e-1031


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)
MA0003.10.0370565
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.114225
MA0017.11.9612
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.11.12059
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.0496191
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.11.64924
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.943943
MA0069.10.776171
MA0070.10.765217
MA0071.11.05086
MA0072.10.760818
MA0073.10.304769
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.0234479
MA0089.10
MA0090.10.291627
MA0091.10.927876
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.11.91523
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.819774
MA0113.10.498009
MA0114.12.0906
MA0115.15.44174
MA0116.11.49522
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.11.14308
MA0139.10.0922451
MA0140.10.405425
MA0141.11.33697
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.115359
MA0146.10.700193
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.0944823
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.118985
MA0047.21.18756
MA0112.20.106997
MA0065.21.6488
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.634487
MA0155.11.09568
MA0156.10.654264
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.826158
MA0164.10.509774
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.20.000645997
MA0102.21.32663
MA0258.10.135061
MA0259.10.973858
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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