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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:53, 17 September 2013


Full id: C1835_CD14_Mast_Natural_Eosinophils_Peripheral_immature_Basophils



Phase1 CAGE Peaks

Hg19::chr1:150583933..150583944,-p@chr1:150583933..150583944
-
Hg19::chr1:150584006..150584024,-p1@AK129725
Hg19::chr1:150584301..150584312,+p@chr1:150584301..150584312
+
Hg19::chr1:150584909..150584912,+p@chr1:150584909..150584912
+
Hg19::chr1:204381399..204381426,+p@chr1:204381399..204381426
+


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 monocyte1.37e-7442
CD14-positive, CD16-negative classical monocyte1.37e-7442
leukocyte1.91e-73136
myeloid leukocyte2.20e-6872
defensive cell9.59e-6448
phagocyte9.59e-6448
granulocyte monocyte progenitor cell6.86e-5867
hematopoietic stem cell7.68e-58168
angioblastic mesenchymal cell7.68e-58168
macrophage dendritic cell progenitor7.47e-5561
hematopoietic cell5.99e-54177
hematopoietic lineage restricted progenitor cell1.44e-53120
myeloid lineage restricted progenitor cell3.25e-5366
nongranular leukocyte1.67e-51115
monopoietic cell3.56e-5159
monocyte3.56e-5159
monoblast3.56e-5159
promonocyte3.56e-5159
hematopoietic oligopotent progenitor cell7.53e-50161
hematopoietic multipotent progenitor cell7.53e-50161
myeloid cell8.58e-47108
common myeloid progenitor8.58e-47108
stuff accumulating cell2.91e-3787
connective tissue cell1.87e-25361
mesenchymal cell1.97e-25354
motile cell1.87e-21386
stem cell1.06e-19441
multi fate stem cell2.04e-18427
somatic stem cell6.96e-18433
intermediate monocyte2.83e-159
CD14-positive, CD16-positive monocyte2.83e-159
granulocyte1.02e-148
blood cell2.44e-1011
CD4-positive, alpha-beta T cell4.84e-096
somatic cell7.61e-09588
basophil2.76e-083
mature alpha-beta T cell3.43e-0818
alpha-beta T cell3.43e-0818
immature T cell3.43e-0818
mature T cell3.43e-0818
immature alpha-beta T cell3.43e-0818
neutrophil4.64e-083
natural killer cell5.72e-083
pro-NK cell5.72e-083
single nucleate cell2.98e-073
mononuclear cell2.98e-073
Uber Anatomy
Ontology termp-valuen
bone marrow4.89e-5276
bone element2.81e-4782
hematopoietic system1.22e-4598
blood island1.22e-4598
skeletal element7.35e-4490
immune system2.34e-4293
hemolymphoid system4.12e-40108
skeletal system3.81e-38100
connective tissue3.14e-24371
musculoskeletal system1.42e-18167
lateral plate mesoderm1.35e-16203
mesoderm4.20e-07315
mesoderm-derived structure4.20e-07315
presumptive mesoderm4.20e-07315


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.14.08995
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.13.64286
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.16.69924
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.15.03975
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.11.35623
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.13.1409
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.22.8068
MA0079.28.2878
MA0102.23.62459
MA0258.10.345771
MA0259.10.395396
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
BATF#10538314.61468107538220.0006498237314125670.00532331482351534
BCL11A#53335317.02167306216420.000414967457127050.00390474693710172
CEBPB#105146.376918100659850.001113944176677320.00765439935969486
EP300#203345.419153380978560.00209386927943890.0121180102890014
FOS#235335.398773185336640.01153895317278740.0421930092575011
FOSL2#2355413.54416048364945.7953819349229e-050.000964717714219657
FOXA1#316948.865135799508360.0003075468591372710.00316732929902746
FOXA2#3170314.77827825159910.0006289192851194480.00517438957134
GABPB1#255345.654147068945740.001776696502096670.0109099486113872
GATA2#262437.64695904013240.004279061879252130.0203303131474485
GTF2F1#2962410.19172870140610.000177833889427640.00215887406462087
HNF4A#3172313.87937421777220.0007561408847434270.0059456857296882
HNF4G#3174317.25205351586810.0003988503772822420.00389558912868045
IRF4#3662313.14870761204650.0008860469322808430.00660465745203619
JUN#3725410.01026335386910.0001908531347801070.00230566923577785
JUND#372745.595731153496820.001849593301755460.0109345451625743
MAFF#23764333.78921389396715.44627740085589e-050.000923232860684935
MEF2A#4205311.24593854578640.001399366787411950.0091035547471357
MXI1#460147.969257303007440.0004668546380070170.00429508734485684
NFKB1#479044.390450739355070.004707732692524960.0222043487637002
NR3C1#290838.983813998703820.002687995788940450.0147963733832895
POU2F2#545235.463674434645510.01115650094469780.0410185806577233
REST#597847.720022972902420.0005286363773650570.00457341406690103
RFX5#599349.638328661756080.000221480125815720.00249688718264982
SIN3A#2594244.327107781452110.004977052855762880.0232457592774482
SMARCC1#6599326.19801559177890.0001159625626060410.00157674965186985
SMARCC2#6601356.49322465613861.17726327391127e-050.000298355251307982
SP1#666744.558705102512720.00407573565781680.019486621331566
SPI1#668846.563458806818180.0009957429636454020.00714247248490125
SRF#672238.278306957300690.003404846073776150.0173632187060111
STAT3#677448.415571997723390.0003771527211598630.00374282146001662



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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