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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0103309215386236,0

Latest revision as of 12:39, 17 September 2013


Full id: C4091_mature_CD14CD16_Dendritic_migratory_CD14_immature_Basophils



Phase1 CAGE Peaks

Hg19::chr22:25960595..25960655,+p1@ADRBK2
Hg19::chr22:25960662..25960688,+p3@ADRBK2
Hg19::chr22:25960941..25961006,+p4@ADRBK2


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
leukocyte5.83e-46136
hematopoietic stem cell1.72e-43168
angioblastic mesenchymal cell1.72e-43168
hematopoietic cell1.47e-40177
hematopoietic oligopotent progenitor cell2.44e-40161
hematopoietic multipotent progenitor cell2.44e-40161
myeloid leukocyte7.94e-3972
myeloid cell2.05e-36108
common myeloid progenitor2.05e-36108
granulocyte monocyte progenitor cell3.37e-3667
nongranular leukocyte9.77e-36115
hematopoietic lineage restricted progenitor cell1.23e-35120
macrophage dendritic cell progenitor2.91e-3561
monopoietic cell5.92e-3459
monocyte5.92e-3459
monoblast5.92e-3459
promonocyte5.92e-3459
myeloid lineage restricted progenitor cell7.81e-3466
defensive cell1.02e-3048
phagocyte1.02e-3048
classical monocyte2.52e-2742
CD14-positive, CD16-negative classical monocyte2.52e-2742
stuff accumulating cell2.73e-2087
lymphocyte of B lineage1.74e-0824
pro-B cell1.74e-0824
intermediate monocyte9.16e-089
CD14-positive, CD16-positive monocyte9.16e-089
dendritic cell1.66e-0710
conventional dendritic cell3.59e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.02e-3598
blood island2.02e-3598
hemolymphoid system9.67e-30108
bone marrow4.03e-2976
bone element2.16e-2782
immune system5.85e-2493
skeletal element4.07e-2390
adult organism7.90e-23114
skeletal system1.06e-18100
neural tube2.80e-1156
neural rod2.80e-1156
future spinal cord2.80e-1156
neural keel2.80e-1156
regional part of nervous system1.22e-1053
regional part of brain1.22e-1053
regional part of forebrain2.45e-0941
forebrain2.45e-0941
anterior neural tube2.45e-0941
future forebrain2.45e-0941
regional part of cerebral cortex3.41e-0922
neocortex2.20e-0820
brain3.51e-0868
future brain3.51e-0868
brain grey matter4.46e-0834
gray matter4.46e-0834
telencephalon5.07e-0834
central nervous system8.29e-0881
cerebral hemisphere8.34e-0832
regional part of telencephalon1.66e-0732
nervous system4.22e-0789
cerebral cortex8.67e-0725
pallium8.67e-0725


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)
MA0003.13.22681
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0057.13.3282
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
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
MA0100.12.19699
MA0101.10.646932
MA0103.10.628063
MA0105.13.21605
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.17
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
E2F6#187635.017155731697390.00791769806886330.032296378246134
EBF1#187938.9064668465690.00141523283560980.00916509593341926
HNF4A#3172323.13229036295378.07584663437677e-050.00122949467441352
HNF4G#3174328.75342252644684.20470658818262e-050.000757783177503373
MYC#460935.22228187160940.007020843755740150.0295034764819437
NRF1#4899312.21027944771090.0005492172401020010.00471785650098806
SIN3A#2594235.408884726815140.006318961977991520.027732322142264
ZBTB7A#5134137.35190930787590.002516255860282270.0140494651586217
ZNF263#1012738.221841637010680.001799043925565870.0109608183725455



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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