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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:12, 17 September 2013


Full id: C2741_B_CD14_splenic_immature_b_Mast_xeroderma



Phase1 CAGE Peaks

Hg19::chr3:47032417..47032436,+p@chr3:47032417..47032436
+
Hg19::chr7:20259717..20259736,-p@chr7:20259717..20259736
-
Hg19::chr9:128394685..128394703,-p@chr9:128394685..128394703
-
Hg19::chrX:13024034..13024045,+p@chrX:13024034..13024045
+


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

No GOStat results

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
classical monocyte2.17e-6542
CD14-positive, CD16-negative classical monocyte2.17e-6542
defensive cell1.73e-5648
phagocyte1.73e-5648
nongranular leukocyte1.34e-48115
leukocyte1.18e-47136
macrophage dendritic cell progenitor3.33e-4661
monopoietic cell5.06e-4459
monocyte5.06e-4459
monoblast5.06e-4459
promonocyte5.06e-4459
hematopoietic lineage restricted progenitor cell1.06e-43120
granulocyte monocyte progenitor cell1.36e-4167
hematopoietic cell4.53e-39177
myeloid lineage restricted progenitor cell8.20e-3966
myeloid leukocyte3.82e-3872
hematopoietic stem cell3.64e-37168
angioblastic mesenchymal cell3.64e-37168
hematopoietic oligopotent progenitor cell9.16e-35161
hematopoietic multipotent progenitor cell9.16e-35161
stuff accumulating cell1.51e-2887
myeloid cell7.58e-28108
common myeloid progenitor7.58e-28108
mesenchymal cell1.52e-13354
connective tissue cell3.97e-13361
circulating cell3.78e-126
motile cell1.18e-11386
lymphocyte of B lineage1.67e-1124
pro-B cell1.67e-1124
multi fate stem cell7.48e-10427
somatic stem cell1.33e-09433
stem cell2.78e-09441
intermediate monocyte1.02e-089
CD14-positive, CD16-positive monocyte1.02e-089
lymphoid lineage restricted progenitor cell3.32e-0752
lymphocyte4.91e-0753
common lymphoid progenitor4.91e-0753
single nucleate cell6.47e-073
mononuclear cell6.47e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.78e-3998
blood island2.78e-3998
bone marrow5.01e-3676
hemolymphoid system4.76e-35108
bone element5.51e-3382
immune system5.69e-3193
skeletal element1.48e-2990
skeletal system4.95e-26100
lateral plate mesoderm1.58e-15203
musculoskeletal system2.84e-13167
connective tissue1.47e-12371
mesoderm1.24e-07315
mesoderm-derived structure1.24e-07315
presumptive mesoderm1.24e-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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
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
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
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
MA0073.10.00636811
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
MA0100.11.9583
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
MA0119.11.43218
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
MA0142.12.2938
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.11.53138
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
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0021048
MA0102.21.75932
MA0258.10.418966
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

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

TF#promotersEnrichmentp-valueq-value
BATF#10538318.26835134422770.0002681660105721290.00286780565002484
BCL11A#53335428.36945510360711.542446414682e-065.89862911398658e-05
BCLAF1#9774210.82632380506090.01202203816432580.043662875359717
CHD2#110637.758017125587640.003351522464536340.0173059257724568
EBF1#187948.9064668465690.00015887907472010.00199917731140874
EP300#203346.77394172622320.0004748459821442640.00434830684166285
HNF4A#3172211.56614518147680.01057585681762490.0390763429624259
HNF4G#3174214.37671126322340.006924169980439180.0293095038538924
IRF4#3662316.43588451505810.0003669431395554610.003659585041256
MEF2A#4205418.74323090964418.0978922767748e-060.000224571367895402
MEF2C#4208330.9835158694685.56692972943475e-050.00094185092177618
NFKB1#479045.488063424193840.001102199566301980.0076885266166853
PAX5#507946.669565531177830.0005052774169483260.00444571761993818
PBX3#5090210.95725634337210.01174530180688030.0428590047660381
POU2F2#545249.106124057742520.000145395665174930.00188539581266507
SP1#666745.69838137814090.0009482606065333980.00685223756214914
SPI1#668848.204323508522730.000220661881527680.00249709678674498
TCF12#693837.975848676639820.003090920396013070.0162863949971853



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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