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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 14:15, 17 September 2013


Full id: C4548_CD14_Neutrophils_Basophils_granulocyte_Dendritic_Eosinophils_blood



Phase1 CAGE Peaks

Hg19::chr6:11537971..11538030,+p1@TMEM170B
Hg19::chr6:11538045..11538058,+p3@TMEM170B
Hg19::chr6:11538902..11538907,-p@chr6:11538902..11538907
-


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
hematopoietic stem cell2.49e-36168
angioblastic mesenchymal cell2.49e-36168
leukocyte3.71e-36136
myeloid leukocyte6.07e-3672
defensive cell3.71e-3448
phagocyte3.71e-3448
hematopoietic cell3.61e-33177
classical monocyte6.99e-3342
CD14-positive, CD16-negative classical monocyte6.99e-3342
hematopoietic oligopotent progenitor cell2.12e-31161
hematopoietic multipotent progenitor cell2.12e-31161
nongranular leukocyte1.36e-29115
myeloid cell2.21e-29108
common myeloid progenitor2.21e-29108
monopoietic cell8.49e-2959
monocyte8.49e-2959
monoblast8.49e-2959
promonocyte8.49e-2959
granulocyte monocyte progenitor cell4.61e-2867
myeloid lineage restricted progenitor cell3.45e-2766
macrophage dendritic cell progenitor3.64e-2761
hematopoietic lineage restricted progenitor cell1.48e-25120
stuff accumulating cell2.23e-1687
intermediate monocyte3.24e-099
CD14-positive, CD16-positive monocyte3.24e-099
granulocyte4.64e-098
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.60e-2898
blood island2.60e-2898
hemolymphoid system8.29e-24108
bone marrow3.95e-2376
bone element3.52e-2282
immune system4.64e-1993
skeletal element2.86e-1890
skeletal system4.34e-15100
adult organism3.19e-10114
neural tube4.84e-0956
neural rod4.84e-0956
future spinal cord4.84e-0956
neural keel4.84e-0956
regional part of nervous system1.36e-0853
regional part of brain1.36e-0853
central nervous system1.78e-0881
nervous system6.98e-0889
regional part of forebrain8.02e-0841
forebrain8.02e-0841
anterior neural tube8.02e-0841
future forebrain8.02e-0841
cerebral hemisphere1.83e-0732
brain2.04e-0768
future brain2.04e-0768
telencephalon2.62e-0734
brain grey matter3.96e-0734
gray matter3.96e-0734


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)
MA0003.12.05336
MA0004.10.826076
MA0006.12.61424
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
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
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
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
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
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
MA0139.12.91906
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
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
NFYA#4800212.28372046655370.008516011403724430.0324931943224308
NFYB#4801211.17319550235760.01025467135054530.0381541724681011
SMARCB1#6598212.16847718743830.008675002221921740.0330117892896806
SREBF1#6720231.33723296032550.00133816265136180.00887792968781447
SREBF2#67212291.2955082742321.56525677906814e-050.00036645113819569
THAP1#55145220.91276306856750.002983447413736940.0158771090162177



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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