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{{Coexpression_clusters
{
|full_id=C2037_migratory_Neutrophils_Eosinophils_immature_lymphoma_CD14_splenic
 

Latest revision as of 11:57, 17 September 2013


Full id: C2037_migratory_Neutrophils_Eosinophils_immature_lymphoma_CD14_splenic



Phase1 CAGE Peaks

Hg19::chr10:11207485..11207496,+p9@CELF2
Hg19::chr13:46756351..46756390,-p2@LCP1
Hg19::chr14:89953003..89953049,-p@chr14:89953003..89953049
-
Hg19::chr2:158300487..158300500,-p3@CYTIP


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:0001891phagocytic cup0.00117744024490757
GO:0051017actin filament bundle formation0.00843832175517092
GO:0005884actin filament0.00843832175517092
GO:0051015actin filament binding0.00843832175517092
GO:0007015actin filament organization0.00843832175517092
GO:0001726ruffle0.00843832175517092
GO:0031252leading edge0.0121108139476207
GO:0030036actin cytoskeleton organization and biogenesis0.0335035269687336
GO:0030029actin filament-based process0.0335035269687336
GO:0015629actin cytoskeleton0.0335035269687336
GO:0042995cell projection0.0335035269687336
GO:0042802identical protein binding0.035715687428863
GO:0003779actin binding0.039670679020732
GO:0005829cytosol0.0473330978452843
GO:0008092cytoskeletal protein binding0.0473330978452843



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 cell3.79e-93168
angioblastic mesenchymal cell3.79e-93168
hematopoietic cell1.43e-88177
hematopoietic oligopotent progenitor cell6.61e-88161
hematopoietic multipotent progenitor cell6.61e-88161
leukocyte1.23e-86136
hematopoietic lineage restricted progenitor cell1.16e-70120
nongranular leukocyte2.92e-69115
myeloid cell1.80e-58108
common myeloid progenitor1.80e-58108
myeloid leukocyte2.46e-5072
granulocyte monocyte progenitor cell2.85e-4567
myeloid lineage restricted progenitor cell5.07e-4366
macrophage dendritic cell progenitor9.66e-4361
monopoietic cell5.37e-4159
monocyte5.37e-4159
monoblast5.37e-4159
promonocyte5.37e-4159
defensive cell1.35e-3748
phagocyte1.35e-3748
classical monocyte7.00e-3542
CD14-positive, CD16-negative classical monocyte7.00e-3542
nucleate cell2.60e-2455
lymphocyte3.57e-2453
common lymphoid progenitor3.57e-2453
lymphoid lineage restricted progenitor cell1.13e-2352
mesenchymal cell8.91e-17354
connective tissue cell1.92e-15361
stuff accumulating cell4.38e-1387
lymphocyte of B lineage8.94e-1224
pro-B cell8.94e-1224
T cell2.14e-1125
pro-T cell2.14e-1125
motile cell3.07e-11386
mature alpha-beta T cell2.11e-1018
alpha-beta T cell2.11e-1018
immature T cell2.11e-1018
mature T cell2.11e-1018
immature alpha-beta T cell2.11e-1018
dendritic cell5.24e-1010
conventional dendritic cell6.48e-098
intermediate monocyte8.82e-099
CD14-positive, CD16-positive monocyte8.82e-099
granulocyte2.34e-088
B cell3.57e-0814
multi fate stem cell5.45e-07427
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.25e-5298
blood island2.25e-5298
hemolymphoid system2.14e-46108
bone marrow6.93e-3976
immune system8.74e-3793
bone element9.41e-3482
skeletal element4.61e-2890
skeletal system1.13e-23100
adult organism3.86e-16114
connective tissue2.19e-14371
lateral plate mesoderm2.09e-12203
blood3.24e-1015
haemolymphatic fluid3.24e-1015
organism substance3.24e-1015
Disease
Ontology termp-valuen
hematologic cancer1.27e-1051
immune system cancer1.27e-1051
leukemia1.36e-0839
myeloid leukemia4.73e-0731


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.11.07498
MA0259.10.471671
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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