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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:29, 17 September 2013


Full id: C704_Eosinophils_CD14CD16_Neutrophils_CD14_CD4_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr17:2303458..2303472,+p@chr17:2303458..2303472
+
Hg19::chr17:2303504..2303517,+p@chr17:2303504..2303517
+
Hg19::chr17:2303522..2303540,+p@chr17:2303522..2303540
+
Hg19::chr19:12893132..12893144,-p@chr19:12893132..12893144
-
Hg19::chr19:12893177..12893196,-p@chr19:12893177..12893196
-
Hg19::chr1:12234102..12234139,+p@chr1:12234102..12234139
+
Hg19::chr1:244211415..244211427,-p@chr1:244211415..244211427
-
Hg19::chr2:220041798..220041847,+p@chr2:220041798..220041847
+
Hg19::chr5:1386102..1386116,+p@chr5:1386102..1386116
+
Hg19::chr5:98265529..98265551,+p@chr5:98265529..98265551
+
Hg19::chr5:98265553..98265578,+p@chr5:98265553..98265578
+
Hg19::chr6:170862932..170862947,+p5@TBP


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
leukocyte3.03e-69136
classical monocyte2.32e-5642
CD14-positive, CD16-negative classical monocyte2.32e-5642
nongranular leukocyte9.49e-53115
hematopoietic lineage restricted progenitor cell1.30e-52120
hematopoietic stem cell3.09e-52168
angioblastic mesenchymal cell3.09e-52168
myeloid leukocyte2.03e-4972
hematopoietic cell3.52e-48177
hematopoietic oligopotent progenitor cell1.02e-47161
hematopoietic multipotent progenitor cell1.02e-47161
defensive cell2.01e-4748
phagocyte2.01e-4748
granulocyte monocyte progenitor cell5.69e-4067
macrophage dendritic cell progenitor2.35e-3961
monopoietic cell7.72e-3759
monocyte7.72e-3759
monoblast7.72e-3759
promonocyte7.72e-3759
myeloid lineage restricted progenitor cell1.08e-3666
myeloid cell2.15e-32108
common myeloid progenitor2.15e-32108
stuff accumulating cell8.25e-2087
mature alpha-beta T cell2.50e-1618
alpha-beta T cell2.50e-1618
immature T cell2.50e-1618
mature T cell2.50e-1618
immature alpha-beta T cell2.50e-1618
intermediate monocyte2.82e-159
CD14-positive, CD16-positive monocyte2.82e-159
mesenchymal cell2.39e-14354
lymphoid lineage restricted progenitor cell8.28e-1452
connective tissue cell1.40e-13361
granulocyte1.48e-138
lymphocyte2.14e-1353
common lymphoid progenitor2.14e-1353
nucleate cell1.28e-1255
T cell7.15e-1225
pro-T cell7.15e-1225
motile cell2.24e-11386
CD4-positive, alpha-beta T cell1.46e-106
blood cell2.72e-0911
CD8-positive, alpha-beta T cell3.33e-0911
multi fate stem cell8.13e-08427
stem cell1.26e-07441
somatic stem cell2.11e-07433
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.66e-4598
blood island1.66e-4598
hemolymphoid system2.03e-39108
bone marrow1.87e-3676
immune system1.46e-3393
bone element1.31e-3282
skeletal element2.68e-2890
skeletal system6.59e-24100
lateral plate mesoderm1.00e-14203
connective tissue1.52e-12371
musculoskeletal system1.08e-08167


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)
MA0003.11.61997
MA0004.10.861826
MA0006.15.80196
MA0007.10.305951
MA0009.10.756202
MA0014.12.20911
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.357781
MA0050.10.837296
MA0051.11.85986
MA0052.10.682867
MA0055.10.226943
MA0056.10
MA0057.10.3421
MA0058.11.25545
MA0059.10.239727
MA0060.10.103131
MA0061.10.0856761
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.678645
MA0074.11.05467
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.970753
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.558691
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.181541
MA0105.10.563165
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.761158
MA0113.10.467266
MA0114.10.418165
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.11.20117
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.961223
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.441471
MA0146.10.246584
MA0147.10.865676
MA0148.10.910784
MA0149.10.367947
MA0062.20.280813
MA0035.20.376007
MA0039.21.49604
MA0138.20.503176
MA0002.20.652621
MA0137.20.20663
MA0104.21.13554
MA0047.20.440861
MA0112.21.00671
MA0065.20.23889
MA0150.10.723395
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.875403
MA0155.10.202876
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.867657
MA0160.10.357736
MA0161.10
MA0162.16.53764
MA0163.10.180333
MA0164.10.478818
MA0080.20.558855
MA0018.20.453345
MA0099.20.382887
MA0079.21.8736
MA0102.21.28978
MA0258.10.117513
MA0259.12.0602
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
CCNT2#90584.224134384641760.0001042269793544080.00145370746484976
CEBPB#105163.985573812912410.001827907733545880.0108247253222839
CHD2#110665.172011417058430.0004497895363246330.00418416045107405
CTCF#1066462.680128186537510.01385375074811150.0487293504776375
E2F1#186983.271592809919550.000663878513766830.00542738223869229
E2F6#187693.762866798773046.04050132232551e-050.000991768460308683
EBF1#187985.937644564379348.2084546063492e-060.00022703463734971
EGR1#195893.74113432110766.33970241327135e-050.00103406556354778
ELF1#199772.483890475971060.009986512778965350.0374580307471039
HEY1#2346272.356731441811660.01346982061264720.0475808223961394
HMGN3#932485.452365148900391.56099565068508e-050.000365781522912046
MYC#460993.916711403707054.32027414396341e-050.000770368979548223
NR3C1#290867.486511665586525.75824923499379e-050.000960066717518386
PAX5#507963.334782765588910.004629821511058920.0218625459507837
PBX3#5090610.95725634337216.55956664029628e-060.000193305468494894
POLR2A#5430101.789544313798390.01056859658770230.0390536623508842
PRDM1#639221.97182596291010.003608092359441310.0182632461555611
SIN3A#2594262.704442363407570.01325491342780750.0468882910000943
SMARCC1#6599310.91583982990790.002261599214152550.0128424945806263
SPI1#668864.102161754261360.001568896548030080.00995044553225926
TAF1#687282.228697523830190.009307457816451660.0351584775351705
TBP#690892.780078015322290.000724921312220490.00578292521593307
ZBTB7A#5134174.288613762927610.0003629129921758860.00362458353159198
ZEB1#693545.629477339181290.0041376490332310.0197194454404314



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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