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

Latest revision as of 11:40, 17 September 2013


Full id: C1215_migratory_CD19_adult_immature_Dendritic_Burkitt_vein



Phase1 CAGE Peaks

Hg19::chr16:10972516..10972521,+p@chr16:10972516..10972521
+
Hg19::chr1:151319654..151319698,-p2@RFX5
Hg19::chr6:150954152..150954194,+p@chr6:150954152..150954194
+
Hg19::chr6:32977327..32977330,-p3@HLA-DOA
Hg19::chr6:32977332..32977343,-p2@HLA-DOA
Hg19::chr6:32977345..32977394,-p1@HLA-DOA
Hg19::chr6:33080222..33080247,+p1@HLA-DPB2


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
2.20729154564608e-050.0139721554839397278Antigen processing and presentation (KEGG):04612
0.0001207720034001940.03822433907616132182Tuberculosis (KEGG):05152



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:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class II0.00128981675613196
GO:0042613MHC class II protein complex0.00128981675613196
GO:0042611MHC protein complex0.00609127997386628
GO:0019882antigen processing and presentation0.00609127997386628
GO:0032395MHC class II receptor activity0.0174762390536148
GO:0006955immune response0.0328749366611706
GO:0002376immune system process0.0381426036666276



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
leukocyte1.17e-56136
nongranular leukocyte6.80e-53115
hematopoietic lineage restricted progenitor cell3.23e-46120
hematopoietic cell4.08e-44177
hematopoietic stem cell1.08e-43168
angioblastic mesenchymal cell1.08e-43168
hematopoietic oligopotent progenitor cell1.11e-38161
hematopoietic multipotent progenitor cell1.11e-38161
lymphocyte1.63e-3253
common lymphoid progenitor1.63e-3253
lymphoid lineage restricted progenitor cell2.31e-3152
nucleate cell8.92e-3155
lymphocyte of B lineage1.03e-2824
pro-B cell1.03e-2824
B cell8.93e-2014
macrophage dendritic cell progenitor2.17e-1961
monopoietic cell1.31e-1759
monocyte1.31e-1759
monoblast1.31e-1759
promonocyte1.31e-1759
classical monocyte9.04e-1742
CD14-positive, CD16-negative classical monocyte9.04e-1742
granulocyte monocyte progenitor cell1.41e-1667
defensive cell6.13e-1648
phagocyte6.13e-1648
myeloid leukocyte1.77e-1572
myeloid lineage restricted progenitor cell1.47e-1466
dendritic cell1.80e-1410
conventional dendritic cell3.63e-128
myeloid cell9.26e-12108
common myeloid progenitor9.26e-12108
circulating cell1.32e-086
immature conventional dendritic cell4.04e-085
common dendritic progenitor4.04e-085
Langerhans cell5.28e-085
T cell4.65e-0725
pro-T cell4.65e-0725
mesenchymal cell5.15e-07354
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.15e-2798
blood island2.15e-2798
hemolymphoid system1.10e-25108
immune system3.82e-1793
bone marrow3.62e-1476
bone element2.76e-1282
blood1.94e-1115
haemolymphatic fluid1.94e-1115
organism substance1.94e-1115
skeletal element3.29e-1090
adult organism4.27e-10114
skeletal system1.01e-08100
hemopoietic organ4.34e-077
immune organ4.34e-077
Disease
Ontology termp-valuen
lymphoma1.18e-0810


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)
MA0003.10.213534
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.12.51051
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.11.22833
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.11.84146
MA0060.13.44755
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.12.20119
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.11.46532
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.695228
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.12.13665
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.12.34428
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.0610556
MA0147.10.281049
MA0148.11.30922
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.854285
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.282161
MA0150.11.10099
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.0109305
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NFKB1#479064.704054363594720.000216115061401970.00247758956067622
POU2F2#545256.504374326958950.0002767851340330550.00294850699849839
RFX5#599358.605650590853647.16524263203101e-050.00112751359838283
SRF#672235.913076398071920.01066868130167450.0393956230408933



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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