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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:38, 17 September 2013


Full id: C1150_CD14_thymus_hepatoblastoma_CD4_CD34_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr11:66079886..66079899,-p@chr11:66079886..66079899
-
Hg19::chr12:56497962..56497992,-p@chr12:56497962..56497992
-
Hg19::chr12:58335075..58335078,-p@chr12:58335075..58335078
-
Hg19::chr19:12662565..12662577,+p@chr19:12662565..12662577
+
Hg19::chr19:12792137..12792141,+p@chr19:12792137..12792141
+
Hg19::chr5:43604130..43604134,+p@chr5:43604130..43604134
+
Hg19::chr9:19049284..19049297,-p@chr9:19049284..19049297
-


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 cell2.12e-51168
angioblastic mesenchymal cell2.12e-51168
hematopoietic cell2.20e-50177
hematopoietic oligopotent progenitor cell1.29e-45161
hematopoietic multipotent progenitor cell1.29e-45161
leukocyte3.97e-44136
hematopoietic lineage restricted progenitor cell2.55e-41120
nongranular leukocyte2.61e-39115
classical monocyte2.83e-3442
CD14-positive, CD16-negative classical monocyte2.83e-3442
myeloid cell8.06e-31108
common myeloid progenitor8.06e-31108
defensive cell6.21e-2848
phagocyte6.21e-2848
myeloid lineage restricted progenitor cell1.27e-2766
granulocyte monocyte progenitor cell7.52e-2767
macrophage dendritic cell progenitor2.57e-2561
monopoietic cell3.87e-2459
monocyte3.87e-2459
monoblast3.87e-2459
promonocyte3.87e-2459
myeloid leukocyte6.17e-2472
nucleate cell4.25e-1455
mesenchymal cell4.77e-13354
lymphocyte5.16e-1353
common lymphoid progenitor5.16e-1353
connective tissue cell1.27e-12361
lymphoid lineage restricted progenitor cell1.61e-1252
motile cell4.49e-12386
stuff accumulating cell3.06e-1087
T cell7.25e-0825
pro-T cell7.25e-0825
stem cell2.89e-07441
CD4-positive, alpha-beta T cell3.40e-076
multi fate stem cell3.70e-07427
somatic stem cell6.17e-07433
dendritic cell7.10e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.79e-2498
blood island2.79e-2498
bone marrow1.12e-2276
immune system6.37e-2293
bone element1.44e-2182
hemolymphoid system8.86e-21108
skeletal element4.93e-1890
skeletal system1.70e-14100
connective tissue2.35e-11371
Disease
Ontology termp-valuen
hematologic cancer6.47e-1151
immune system cancer6.47e-1151
leukemia8.53e-0839
lymphoma1.00e-0710
cancer1.18e-07235
organ system cancer2.94e-07137
disease of cellular proliferation4.41e-07239


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)
MA0003.10.546816
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.12.12603
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.11.67753
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.11.19421
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.126287
MA0074.10.60198
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.11.90477
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
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.760835
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
MA0139.10.186511
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.828373
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.23.59026
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.556641
MA0065.20.996317
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.485816
MA0163.10.632664
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.21.35081
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
BCLAF1#977439.279706118623640.00299499233575710.0159198902969328
CHD2#110645.910870190923920.002402754466874550.0135512082171893
E2F6#187664.300419198597760.000363797504290860.00363237548285211
GABPB1#255344.038676477818380.00980113494696150.0368460722337465
GTF2F1#296235.459854661467560.0132988216841570.0470229081447565
HEY1#2346252.885793602218360.01231366941853030.0446242867692107
HMGN3#932444.673455841914620.005751881099938870.0259076512785835
HNF4A#317239.913838726980150.002478654821661540.0139221378358346
IRF1#365955.455116966831360.00064157947210550.00525907844652903
MAX#414954.608968220719370.001424337014033610.0091785236878297
NFKB1#479053.92004530299560.003036581424484610.0161171686431747
POLR2A#543072.147453176558070.004747636447610280.0223290283235148
POU2F2#545245.203499461567160.003866714310179810.0190632447054791
SP1#666754.070272412957780.002549206128991580.0141089845737017
TBP#690863.177232017511190.002074112051852660.0120169859416088
TFAP2C#702246.176702062777270.002036754928069020.0118281054232985
ZBTB33#10009313.57059644142050.001001397628590070.00717711823581654
ZBTB7A#5134144.201091033071940.00849410661287350.0324262007654761



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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