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{{Coexpression_clusters
{
|full_id=C4697_Eosinophils_Mast_acute_non_CD14_Neutrophils_myelodysplastic
 

Latest revision as of 14:18, 17 September 2013


Full id: C4697_Eosinophils_Mast_acute_non_CD14_Neutrophils_myelodysplastic



Phase1 CAGE Peaks

Hg19::chr7:73624251..73624266,+p3@LAT2
Hg19::chr7:73624276..73624306,+p2@LAT2
Hg19::chr7:73624327..73624350,+p1@LAT2


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 cell4.78e-72168
angioblastic mesenchymal cell4.78e-72168
hematopoietic oligopotent progenitor cell2.69e-69161
hematopoietic multipotent progenitor cell2.69e-69161
hematopoietic cell4.71e-65177
leukocyte5.04e-60136
myeloid cell1.05e-54108
common myeloid progenitor1.05e-54108
hematopoietic lineage restricted progenitor cell2.29e-52120
nongranular leukocyte1.33e-49115
myeloid leukocyte1.10e-4672
granulocyte monocyte progenitor cell5.11e-4267
myeloid lineage restricted progenitor cell1.88e-4066
macrophage dendritic cell progenitor5.87e-3761
monopoietic cell2.86e-3659
monocyte2.86e-3659
monoblast2.86e-3659
promonocyte2.86e-3659
defensive cell1.77e-3248
phagocyte1.77e-3248
classical monocyte3.79e-2842
CD14-positive, CD16-negative classical monocyte3.79e-2842
lymphocyte of B lineage4.12e-1624
pro-B cell4.12e-1624
nucleate cell3.74e-1355
lymphocyte5.96e-1353
common lymphoid progenitor5.96e-1353
lymphoid lineage restricted progenitor cell2.19e-1252
B cell2.29e-1014
stuff accumulating cell8.10e-0987
mesenchymal cell7.22e-08354
granulocyte3.38e-078
connective tissue cell3.44e-07361
intermediate monocyte5.25e-079
CD14-positive, CD16-positive monocyte5.25e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.52e-4398
blood island1.52e-4398
hemolymphoid system4.20e-39108
bone marrow6.24e-3676
immune system1.98e-3393
bone element6.08e-3282
skeletal element1.09e-2790
adult organism1.91e-26114
skeletal system8.94e-23100
neural tube8.42e-1156
neural rod8.42e-1156
future spinal cord8.42e-1156
neural keel8.42e-1156
regional part of nervous system7.41e-1053
regional part of brain7.41e-1053
regional part of forebrain3.23e-0941
forebrain3.23e-0941
anterior neural tube3.23e-0941
future forebrain3.23e-0941
lateral plate mesoderm4.34e-09203
brain grey matter5.46e-0834
gray matter5.46e-0834
telencephalon6.80e-0834
regional part of telencephalon2.92e-0732
cerebral hemisphere4.51e-0732
Disease
Ontology termp-valuen
hematologic cancer8.75e-1251
immune system cancer8.75e-1251
myeloid leukemia1.65e-1031
leukemia6.61e-1039


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
MA0014.11.24048
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
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.14.04858
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
MA0062.20.449458
MA0035.20.894194
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
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
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#187938.9064668465690.00141523283560980.00919245613024767
ELF1#199734.258097958807540.01295179875054610.0464931913696392
EP300#203336.77394172622320.003216880500103790.0168497809594433



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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