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{{Coexpression_clusters
{
|full_id=C1172_Neutrophils_Whole_CD14_CD14CD16_Eosinophils_CD19_Dendritic
 

Latest revision as of 11:39, 17 September 2013


Full id: C1172_Neutrophils_Whole_CD14_CD14CD16_Eosinophils_CD19_Dendritic



Phase1 CAGE Peaks

Hg19::chr12:54891496..54891526,+p2@NCKAP1L
Hg19::chr12:7060473..7060507,+p2@PTPN6
Hg19::chr15:73076030..73076121,-p1@ADPGK
Hg19::chr17:43487741..43487772,-p1@ARHGAP27
Hg19::chr19:48758926..48758982,+p1@LOC100505812
Hg19::chr1:153917700..153917766,-p1@DENND4B
Hg19::chr7:6066194..6066222,-p3@EIF2AK1


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

GO IDGO nameFDR corrected p-value
GO:0043843ADP-specific glucokinase activity0.00540886612504415
GO:0046984regulation of hemoglobin biosynthetic process0.00540886612504415
GO:0046986negative regulation of hemoglobin biosynthetic process0.00540886612504415
GO:0045993negative regulation of translational initiation by iron0.00540886612504415
GO:0006447regulation of translational initiation by iron0.00865367629574051
GO:0004694eukaryotic translation initiation factor 2alpha kinase activity0.0120168721704563
GO:0042541hemoglobin biosynthetic process0.0120168721704563
GO:0020027hemoglobin metabolic process0.0120168721704563
GO:0001784phosphotyrosine binding0.0120168721704563
GO:0045309protein phosphorylated amino acid binding0.0129774578675695
GO:0045947negative regulation of translational initiation0.0176934080562542
GO:0051219phosphoprotein binding0.018020002793523
GO:0009605response to external stimulus0.037762056295026



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell1.13e-91168
angioblastic mesenchymal cell1.13e-91168
hematopoietic oligopotent progenitor cell1.09e-86161
hematopoietic multipotent progenitor cell1.09e-86161
hematopoietic cell1.55e-86177
leukocyte1.32e-79136
hematopoietic lineage restricted progenitor cell2.19e-67120
nongranular leukocyte4.01e-65115
myeloid cell1.67e-56108
common myeloid progenitor1.67e-56108
myeloid leukocyte7.83e-4672
granulocyte monocyte progenitor cell5.10e-4167
myeloid lineage restricted progenitor cell5.82e-4066
macrophage dendritic cell progenitor5.60e-3761
monopoietic cell2.76e-3659
monocyte2.76e-3659
monoblast2.76e-3659
promonocyte2.76e-3659
defensive cell4.03e-3348
phagocyte4.03e-3348
classical monocyte2.49e-2842
CD14-positive, CD16-negative classical monocyte2.49e-2842
nucleate cell4.48e-2555
lymphocyte6.79e-2553
common lymphoid progenitor6.79e-2553
lymphoid lineage restricted progenitor cell2.29e-2452
mesenchymal cell3.25e-13354
T cell2.75e-1225
pro-T cell2.75e-1225
lymphocyte of B lineage3.96e-1224
pro-B cell3.96e-1224
connective tissue cell5.03e-12361
mature alpha-beta T cell2.34e-1018
alpha-beta T cell2.34e-1018
immature T cell2.34e-1018
mature T cell2.34e-1018
immature alpha-beta T cell2.34e-1018
stuff accumulating cell7.77e-1087
B cell1.08e-0814
motile cell4.14e-08386
intermediate monocyte1.98e-079
CD14-positive, CD16-positive monocyte1.98e-079
CD8-positive, alpha-beta T cell3.45e-0711
granulocyte5.21e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.88e-4898
blood island3.88e-4898
hemolymphoid system1.89e-43108
bone marrow9.60e-3576
immune system9.46e-3493
bone element5.88e-3082
skeletal element1.14e-2490
adult organism2.40e-24114
skeletal system1.64e-20100
lateral plate mesoderm8.07e-12203
connective tissue8.15e-11371
blood1.53e-1015
haemolymphatic fluid1.53e-1015
organism substance1.53e-1015
Disease
Ontology termp-valuen
hematologic cancer3.40e-1451
immune system cancer3.40e-1451
leukemia6.16e-1339
myeloid leukemia2.72e-1031


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)
MA0003.10.358813
MA0004.10.502801
MA0006.10.341337
MA0007.11.21493
MA0009.10.973289
MA0014.10.610358
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.11.25271
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.649431
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.946606
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.12.03625
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.11.26109
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.11.68581
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.9963
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.12.97215
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.11.04496
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.12.02038
MA0145.10.581146
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.6882
MA0035.20.564239
MA0039.20.854285
MA0138.20.704862
MA0002.20.213296
MA0137.21.70023
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.12.27082
MA0155.10.250175
MA0156.11.7082
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.25944
MA0163.10.382702
MA0164.10.678332
MA0080.21.63199
MA0018.20.650405
MA0099.20.572
MA0079.20.122495
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
EBF1#187945.089409626610860.004198233162502420.0199926712534125
ELF1#199763.649798250406460.0009377479782620690.00678989608303606
GABPB1#255344.038676477818380.00980113494696150.0368473985862387
MEF2C#4208211.80324414074970.01134538181234960.0415988039285206
POLR2A#543072.147453176558070.004747636447610280.0223320453520682
SPI1#668867.032277293019482.05436318006376e-050.000455049069273974
YY1#752864.209574928446160.000411683378865750.00392225874889254



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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