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{{Coexpression_clusters
{
|full_id=C1388_immature_CD14_Basophils_Mast_CD133_Peripheral_Natural

Latest revision as of 11:43, 17 September 2013


Full id: C1388_immature_CD14_Basophils_Mast_CD133_Peripheral_Natural



Phase1 CAGE Peaks

Hg19::chr14:104094662..104094670,+p@chr14:104094662..104094670
+
Hg19::chr19:1021505..1021517,+p1@ENST00000384627
Hg19::chr19:4832054..4832058,+p@chr19:4832054..4832058
+
Hg19::chr19:58695085..58695128,-p@chr19:58695085..58695128
-
Hg19::chr2:153032078..153032096,+p@chr2:153032078..153032096
+
Hg19::chr2:178128451..178128470,+p@chr2:178128451..178128470
+


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
classical monocyte4.32e-3242
CD14-positive, CD16-negative classical monocyte4.32e-3242
leukocyte1.89e-27136
defensive cell1.73e-2648
phagocyte1.73e-2648
myeloid leukocyte3.35e-2572
granulocyte monocyte progenitor cell5.11e-2567
macrophage dendritic cell progenitor2.84e-2361
hematopoietic lineage restricted progenitor cell1.57e-22120
nongranular leukocyte2.98e-22115
monopoietic cell6.87e-2259
monocyte6.87e-2259
monoblast6.87e-2259
promonocyte6.87e-2259
hematopoietic stem cell1.39e-21168
angioblastic mesenchymal cell1.39e-21168
myeloid lineage restricted progenitor cell1.60e-2166
hematopoietic cell2.96e-19177
hematopoietic oligopotent progenitor cell3.31e-19161
hematopoietic multipotent progenitor cell3.31e-19161
myeloid cell2.66e-17108
common myeloid progenitor2.66e-17108
stuff accumulating cell2.83e-1087
native cell9.56e-10722
mesenchymal cell2.21e-09354
animal cell2.27e-09679
eukaryotic cell2.27e-09679
connective tissue cell7.54e-09361
motile cell2.58e-08386
intermediate monocyte5.10e-089
CD14-positive, CD16-positive monocyte5.10e-089
somatic cell5.28e-08588
stem cell1.11e-07441
multi fate stem cell1.29e-07427
somatic stem cell1.96e-07433
Uber Anatomy
Ontology termp-valuen
bone marrow1.45e-2176
bone element8.43e-1982
hematopoietic system1.33e-1798
blood island1.33e-1798
immune system5.41e-1793
skeletal element5.43e-1790
hemolymphoid system4.96e-16108
skeletal system1.12e-14100
lateral plate mesoderm2.48e-09203
connective tissue1.87e-08371
musculoskeletal system1.10e-07167


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.13.53887
MA0042.13.39167
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.11.47313
MA0145.10.347815
MA0146.11.05598
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.82735
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.10486
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
BCL3#602211.51570093457940.01162725346801640.0424772185863355
BDP1#558141175.0255681818180.00569994366159920.0257003158517359
BRF2#552901179.0959302325580.005570700836719840.0252100885989333
CCNT2#90544.224134384641760.007109805478875810.0296092580910882
CTCF#1066443.573504248716680.01316635007238510.0466018380455427
E2F1#186954.089491012399440.001749817597761990.0107581797899961
EBF1#187945.937644564379340.001975153636421710.0114901727084191
ELF1#199753.548414965672950.003446837775721690.0175294259085799
FOSL2#235538.465100302280850.003598315634615090.0182225906300522
HEY1#2346264.040111043105710.0002298968555807510.00253111930212925
MEF2C#4208213.77045149754130.008235596942270060.0324658403749573
NFKB1#479043.658708949462560.01207927289015230.043828070503565
PAX5#507955.557971275981520.0003977176196612860.00388634267213745
POLR2A#543062.147453176558070.01019570676818780.0380146877713315
POLR3G#106221362.4058823529410.002756203817184890.0151152683502926
SIN3A#2594254.507403939012610.001096110061208640.0076593495706255
SMARCB1#659839.126357890578710.002900247150367020.0156771860740738
STAT3#677447.012976664769490.001045723664135530.0073928338021154
TAF1#687263.343046285745290.0007162474284635620.00572948569097013
TCF12#693835.317232451093210.013367345733860.0472444068053672
TRIM28#1015539.295262522631260.00275136505059490.0150911094227762
ZBTB33#10009210.55490834332710.01374250737140590.0483869505549949
ZBTB7A#5134144.901272871917260.004079628118843750.0194864981067424



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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