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

Latest revision as of 11:33, 17 September 2013


Full id: C883_CD14_CD14CD16_Monocytederived_spleen_Macrophage_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:60145301..60145329,-p@chr11:60145301..60145329
-
Hg19::chr11:60145332..60145348,-p@chr11:60145332..60145348
-
Hg19::chr11:60145948..60145960,+p2@MS4A14
p2@MS4A7
Hg19::chr11:60145967..60145978,+p3@MS4A7
Hg19::chr11:60145997..60146040,+p1@MS4A14
p1@MS4A7
Hg19::chr11:60146052..60146068,+p4@MS4A7
Hg19::chr11:60146080..60146091,+p5@MS4A7
Hg19::chr11:60150636..60150652,+p7@MS4A7
Hg19::chr11:60161612..60161616,+p@chr11:60161612..60161616
+


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
monopoietic cell3.88e-6959
monocyte3.88e-6959
monoblast3.88e-6959
promonocyte3.88e-6959
macrophage dendritic cell progenitor9.24e-6961
granulocyte monocyte progenitor cell2.06e-6467
myeloid lineage restricted progenitor cell2.83e-6366
myeloid leukocyte2.86e-6372
defensive cell1.04e-6148
phagocyte1.04e-6148
classical monocyte2.51e-5442
CD14-positive, CD16-negative classical monocyte2.51e-5442
nongranular leukocyte5.79e-48115
leukocyte1.43e-44136
hematopoietic lineage restricted progenitor cell4.47e-44120
myeloid cell5.46e-44108
common myeloid progenitor5.46e-44108
hematopoietic stem cell4.62e-38168
angioblastic mesenchymal cell4.62e-38168
hematopoietic oligopotent progenitor cell5.96e-36161
hematopoietic multipotent progenitor cell5.96e-36161
hematopoietic cell1.23e-34177
stuff accumulating cell1.01e-2687
intermediate monocyte4.50e-139
CD14-positive, CD16-positive monocyte4.50e-139
macrophage1.55e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.35e-7098
blood island4.35e-7098
hemolymphoid system1.70e-64108
bone marrow5.57e-5876
immune system1.44e-5493
bone element4.97e-5282
skeletal element2.40e-4590
skeletal system1.59e-38100
adult organism5.80e-28114
lateral plate mesoderm2.80e-27203
musculoskeletal system1.10e-16167
mesoderm4.70e-13315
mesoderm-derived structure4.70e-13315
presumptive mesoderm4.70e-13315
blood7.54e-1015
haemolymphatic fluid7.54e-1015
organism substance7.54e-1015
organ3.84e-07503
germ layer4.47e-07560
germ layer / neural crest4.47e-07560
embryonic tissue4.47e-07560
presumptive structure4.47e-07560
germ layer / neural crest derived structure4.47e-07560
epiblast (generic)4.47e-07560
tissue4.74e-07773
embryonic structure8.44e-07564


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)
MA0003.10.000472949
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.13.07926
MA0030.10.774581
MA0031.10.710608
MA0038.11.28049
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.42489
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.432181
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.11.94461
MA0078.10.607575
MA0081.11.55973
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.13.62497
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.12.25358
MA0101.10.746654
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.11.11943
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.177438
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.20.46405
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.11.64445
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.225151
MA0155.10.0402662
MA0156.13.04199
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.22.91221
MA0018.20.556211
MA0099.20.481058
MA0079.22.18822e-08
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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
BCL11A#53335515.76080839089286.07835896292738e-060.000180859752629394
BCLAF1#9774512.02924867228992.26104873625909e-050.000494020227962684
EBF1#187976.927251991775896.58055964035478e-060.000192727725260519
MEF2A#4205510.41290606091344.53864389110116e-050.000798267816340038
NFKB1#479053.048924124552130.01316873026498510.046599207838476
PAX5#507975.187439857582764.62776729125731e-050.000812438036866066
SPI1#668876.381140506628791.14766724697107e-050.000292273151929802
SRF#6722710.73113864835273.31352184322677e-071.65658644224395e-05
ZEB1#693559.38246223196887.48833020047875e-050.00116017462959175



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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