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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:44, 17 September 2013


Full id: C1429_CD14_Basophils_Natural_immature_Peripheral_CD14CD16_CD4



Phase1 CAGE Peaks

Hg19::chr17:17743452..17743466,-p@chr17:17743452..17743466
-
Hg19::chr19:39892249..39892258,-p@chr19:39892249..39892258
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Hg19::chr19:39892296..39892314,-p@chr19:39892296..39892314
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Hg19::chr2:235217404..235217432,-p@chr2:235217404..235217432
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Hg19::chr6:109704348..109704364,+p3@BC030091
Hg19::chr9:134553955..134553973,-p@chr9:134553955..134553973
-


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
leukocyte3.23e-80136
hematopoietic stem cell3.57e-63168
angioblastic mesenchymal cell3.57e-63168
classical monocyte5.37e-6242
CD14-positive, CD16-negative classical monocyte5.37e-6242
hematopoietic lineage restricted progenitor cell1.78e-61120
nongranular leukocyte8.25e-61115
hematopoietic cell1.17e-58177
hematopoietic oligopotent progenitor cell1.82e-57161
hematopoietic multipotent progenitor cell1.82e-57161
defensive cell1.81e-5248
phagocyte1.81e-5248
myeloid leukocyte8.08e-5172
granulocyte monocyte progenitor cell5.68e-4667
macrophage dendritic cell progenitor1.63e-4461
myeloid lineage restricted progenitor cell4.49e-4266
monopoietic cell1.88e-4159
monocyte1.88e-4159
monoblast1.88e-4159
promonocyte1.88e-4159
myeloid cell6.37e-39108
common myeloid progenitor6.37e-39108
stuff accumulating cell1.77e-2587
mesenchymal cell7.59e-19354
connective tissue cell5.30e-18361
intermediate monocyte4.06e-179
CD14-positive, CD16-positive monocyte4.06e-179
lymphoid lineage restricted progenitor cell2.65e-1652
lymphocyte7.61e-1653
common lymphoid progenitor7.61e-1653
motile cell1.24e-15386
nucleate cell5.57e-1555
stem cell1.26e-12441
multi fate stem cell1.66e-11427
somatic stem cell1.67e-11433
CD4-positive, alpha-beta T cell9.46e-116
T cell4.35e-1025
pro-T cell4.35e-1025
mature alpha-beta T cell9.61e-1018
alpha-beta T cell9.61e-1018
immature T cell9.61e-1018
mature T cell9.61e-1018
immature alpha-beta T cell9.61e-1018
dendritic cell5.41e-0910
Langerhans cell1.65e-085
granulocyte5.33e-088
basophil4.78e-073
natural killer cell4.78e-073
pro-NK cell4.78e-073
Uber Anatomy
Ontology termp-valuen
bone marrow9.10e-3976
hematopoietic system1.10e-3798
blood island1.10e-3798
immune system5.27e-3593
bone element7.55e-3582
hemolymphoid system1.19e-32108
skeletal element1.91e-3090
skeletal system5.98e-26100
connective tissue1.71e-17371
lateral plate mesoderm9.05e-11203
musculoskeletal system3.54e-10167


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)
MA0003.10.176622
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.882847
MA0058.11.16137
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
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
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.16614
MA0146.10.0213085
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.0929059
MA0138.20.765223
MA0002.22.02127
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.680553
MA0065.20.109623
MA0150.12.10974
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.92418
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.21.69036
MA0099.20.629739
MA0079.20.0146751
MA0102.21.58513
MA0258.10.289793
MA0259.11.6038
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
EP300#203344.515961150815470.005543980051953740.0250956888282766
FOSL2#2355411.28680040304110.0001656657722157630.0020376831450291
GATA1#262336.780154071900220.006765763983348560.0287531892027239
HDAC2#306636.707810118313130.006973940027962660.0294891016875336
JUN#372536.256414596168170.008486346850954870.0324155357606202
JUNB#3726315.30531632991060.0006470753298141560.00530287981563565
MEF2C#4208213.77045149754130.008235596942270060.0324682914595048
NFKB1#479043.658708949462560.01207927289015230.0438311160230219
NR3C1#2908512.47751944264427.52342219908436e-060.000214917585079369
PAX5#507944.446377020785220.005874733519240790.0263632232207274
RFX5#599348.03194055146340.0006204615428381410.0051108433687572
RXRA#6256413.38307809275558.51052088844461e-050.0012763214978005
SMARCC1#6599214.55445310654380.007398079383140510.0305648171484557
SP1#666765.69838137814092.91961319085282e-050.000609721019874981
SREBF2#6721172.82387706855790.01365361575289130.048171406513621
TAF1#687252.785871904787740.01078636340290410.0397935994714012
TBP#690853.088975572580320.006645448275786930.0282890671099255
TCF12#693835.317232451093210.013367345733860.0472460056549664
TCF7L2#693435.385088281568670.01290488779931040.0464077397173809
TFAP2A#702038.259317186522480.003860738477055590.0190454709652453
TFAP2C#702235.404614304930110.01277576166695870.0460623389628027
USF1#739144.240999518138640.007005367750829420.0296052119341591
USF2#739236.49609869253480.007634319815300560.0314574578706768
ZBTB33#10009210.55490834332710.01374250737140590.0483885818874029



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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