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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:09, 17 September 2013


Full id: C2595_Melanocyte_granulocyte_Monocytederived_CD14_acute_CD4_Macrophage



Phase1 CAGE Peaks

Hg19::chr1:6086340..6086351,+p5@KCNAB2
Hg19::chr1:6086354..6086365,+p4@KCNAB2
Hg19::chr1:6086385..6086411,+p1@KCNAB2
Hg19::chr1:6086424..6086442,+p3@KCNAB2


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell6.36e-73168
angioblastic mesenchymal cell6.36e-73168
hematopoietic cell7.23e-70177
hematopoietic oligopotent progenitor cell5.37e-69161
hematopoietic multipotent progenitor cell5.37e-69161
leukocyte5.86e-66136
hematopoietic lineage restricted progenitor cell2.62e-57120
nongranular leukocyte6.65e-57115
myeloid cell1.71e-46108
common myeloid progenitor1.71e-46108
myeloid leukocyte3.99e-4272
granulocyte monocyte progenitor cell1.95e-3867
myeloid lineage restricted progenitor cell1.06e-3766
monopoietic cell9.33e-3659
monocyte9.33e-3659
monoblast9.33e-3659
promonocyte9.33e-3659
macrophage dendritic cell progenitor1.02e-3561
defensive cell6.05e-3148
phagocyte6.05e-3148
classical monocyte1.28e-2642
CD14-positive, CD16-negative classical monocyte1.28e-2642
nucleate cell5.08e-1955
lymphocyte7.32e-1953
common lymphoid progenitor7.32e-1953
lymphoid lineage restricted progenitor cell2.01e-1852
stuff accumulating cell4.05e-1787
T cell2.32e-1125
pro-T cell2.32e-1125
mature alpha-beta T cell1.11e-0818
alpha-beta T cell1.11e-0818
immature T cell1.11e-0818
mature T cell1.11e-0818
immature alpha-beta T cell1.11e-0818
mesenchymal cell1.60e-08354
connective tissue cell1.76e-07361
motile cell1.93e-07386
lymphocyte of B lineage3.13e-0724
pro-B cell3.13e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.79e-4198
blood island2.79e-4198
hemolymphoid system1.65e-35108
bone marrow3.53e-3276
immune system3.35e-2993
bone element1.03e-2682
skeletal element8.47e-2190
skeletal system8.52e-16100
blood4.94e-0715
haemolymphatic fluid4.94e-0715
organism substance4.94e-0715
adult organism6.44e-07114
connective tissue9.54e-07371
Disease
Ontology termp-valuen
hematologic cancer4.35e-1251
immune system cancer4.35e-1251
leukemia1.13e-0939
myeloid leukemia6.85e-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)
MA0003.10.720743
MA0004.10.71247
MA0006.14.49931
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.12.4142
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
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
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
MA0103.12.23207
MA0105.10.232357
MA0106.14.78263
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.12.95284
MA0115.11.45393
MA0116.12.9994
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
MA0144.11.92815
MA0145.11.08195
MA0146.12.92476
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.25.8901
MA0047.20.856092
MA0112.20.187982
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.12.98688
MA0161.10
MA0162.10.0928415
MA0163.13.14178
MA0164.10.90014
MA0080.22.27911
MA0018.20.870662
MA0099.20.7872
MA0079.20.0021048
MA0102.21.75932
MA0258.10.418966
MA0259.14.15404
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
BHLHE40#8553444.87181354697742.46312701995675e-071.28430615495389e-05
E2F1#186944.907389214879320.001724022357361790.0106566744188274
E2F6#187645.017155731697390.00157802193473060.00997500501400127
EBF1#187948.9064668465690.00015887907472010.00199725224900007
ELF1#199744.258097958807540.003041525565781240.0161000450362203
HEY1#2346244.040111043105710.00375304636917980.0186224063925679
MAX#414946.452555509007120.0005767613195645490.00485698882873745
MXI1#460149.96157162875930.0001015224754950450.00142493022688173
MYC#460945.22228187160940.001344309395272740.00888203510678113
NFKB1#479045.488063424193840.001102199566301980.00768288196656292
PAX5#507946.669565531177830.0005052774169483260.00444197543338941
SMARCB1#6598418.25271578115749.00423392720929e-060.000241808482160918
SP1#666745.69838137814090.0009482606065333980.0068474997915883
TAF1#687243.343046285745290.008005664898701650.0322521075588452
TBP#690843.706770687096390.005296377814784350.0244496288277167
TCF12#6938410.63446490218647.8163066689251e-050.00120118783430822
TFAP2A#7020416.5186343730451.34240829060362e-050.000326729851928109
TFAP2C#7022410.80922860986027.32289634782688e-050.00114610515760631
USF1#739146.361499277207960.0006105011399140830.00508332365076034
USF2#7392412.99219738506963.50833029870167e-050.000681559724825341
ZEB1#6935416.88843201754391.22862303393937e-050.000304355220686893



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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