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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 14:15, 17 September 2013


Full id: C4592_acute_myelodysplastic_CD34_CD133_Hodgkin_chronic_CD14CD16



Phase1 CAGE Peaks

Hg19::chr6:31583761..31583786,+p3@AIF1
Hg19::chr6:31583787..31583826,+p2@AIF1
Hg19::chr6:31583836..31583847,+p7@AIF1


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 cell6.47e-72168
angioblastic mesenchymal cell6.47e-72168
hematopoietic oligopotent progenitor cell6.11e-66161
hematopoietic multipotent progenitor cell6.11e-66161
hematopoietic cell2.93e-65177
myeloid cell1.95e-50108
common myeloid progenitor1.95e-50108
leukocyte7.07e-50136
nongranular leukocyte5.29e-44115
hematopoietic lineage restricted progenitor cell5.20e-42120
macrophage dendritic cell progenitor3.80e-3061
granulocyte monocyte progenitor cell2.47e-2967
myeloid leukocyte5.01e-2972
monopoietic cell9.75e-2959
monocyte9.75e-2959
monoblast9.75e-2959
promonocyte9.75e-2959
myeloid lineage restricted progenitor cell1.23e-2766
defensive cell3.84e-2748
phagocyte3.84e-2748
classical monocyte1.59e-2642
CD14-positive, CD16-negative classical monocyte1.59e-2642
nucleate cell6.86e-1455
lymphocyte1.76e-1353
common lymphoid progenitor1.76e-1353
lymphoid lineage restricted progenitor cell6.55e-1352
mature alpha-beta T cell6.64e-1318
alpha-beta T cell6.64e-1318
immature T cell6.64e-1318
mature T cell6.64e-1318
immature alpha-beta T cell6.64e-1318
T cell7.35e-1325
pro-T cell7.35e-1325
CD8-positive, alpha-beta T cell1.49e-0911
stuff accumulating cell5.23e-0987
mesenchymal cell8.40e-09354
intermediate monocyte4.22e-089
CD14-positive, CD16-positive monocyte4.22e-089
connective tissue cell6.10e-08361
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.14e-3398
blood island2.14e-3398
hemolymphoid system1.57e-29108
bone marrow1.78e-2476
immune system5.80e-2493
bone element5.68e-2182
adult organism2.17e-17114
skeletal element4.06e-1790
skeletal system7.95e-14100
neural tube2.63e-0856
neural rod2.63e-0856
future spinal cord2.63e-0856
neural keel2.63e-0856
regional part of nervous system7.24e-0853
regional part of brain7.24e-0853
connective tissue1.34e-07371
regional part of forebrain3.09e-0741
forebrain3.09e-0741
anterior neural tube3.09e-0741
future forebrain3.09e-0741
Disease
Ontology termp-valuen
leukemia1.14e-2039
myeloid leukemia4.25e-2031
hematologic cancer1.88e-1851
immune system cancer1.88e-1851


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.12.0778
MA0072.11.29561
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.13.70241
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.13.4624
MA0117.11.36676
MA0119.12.7939
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.22.07011
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
EBF1#187938.9064668465690.00141523283560980.00918788475901364
MAFK#7975327.10073313782995.02195559325033e-050.000859393773887386
MAX#414936.452555509007120.003721913834265510.0187313492163095
MYC#460935.22228187160940.007020843755740150.0295856157603997
SP1#666735.69838137814090.005403962701712170.0247721748937417
SPI1#668838.204323508522730.001810593189410520.0109386557591742



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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