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Coexpression cluster:C450: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;6:6.64303685244645:0.000201792444037712:0.00239706563499256!BCL11A#53335;5:6.44760343263797:0.000865458559595205:0.00645856566670694!IRF4#3662;5:4.98057106516912:0.00271038957555786:0.0148882541882758!MAX#4149;8:2.34638382145714:0.0137898248043718:0.0485126659057427!MEF2A#4205;6:5.11179024808474:0.000817771050348318:0.00623000880642848!NFKB1#4790;9:2.24511685535202:0.0110949326788116:0.040806580998817!PAX5#5079;9:2.72845862639093:0.00295271953038647:0.0157424613320758!SPI1#6688;14:5.22093314178719:1.94204115573741e-08:1.38921120728808e-06
|tf_chipseq_enrich=BATF#10538;6:6.64303685244645:0.000201792444037712:0.00239706563499256!BCL11A#53335;5:6.44760343263797:0.000865458559595205:0.00645856566670694!IRF4#3662;5:4.98057106516912:0.00271038957555786:0.0148882541882758!MAX#4149;8:2.34638382145714:0.0137898248043718:0.0485126659057427!MEF2A#4205;6:5.11179024808474:0.000817771050348318:0.00623000880642848!NFKB1#4790;9:2.24511685535202:0.0110949326788116:0.040806580998817!PAX5#5079;9:2.72845862639093:0.00295271953038647:0.0157424613320758!SPI1#6688;14:5.22093314178719:1.94204115573741e-08:1.38921120728808e-06
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|tfbs_overrepresentation_for_novel_motifs=0.313352,0.00762177,0.0904779,0.521108,0.528049,0.518467,0.226953,0.111502,0.109134,0.016196,0.916715,0.717665,0.0156564,0.624423,0.524832,0.980021,0.401017,0.403034,0.403831,0.0575111,0.303125,0.129045,0.169484,0.516065,0.368471,0.75697,0.154326,0.168077,0.250879,0.464564,0.141557,0.432083,0.143261,0.191773,0.78124,0.0764988,0.199614,0.999899,1.06784,0.0212383,0.445121,0.131762,0.428928,0.243124,0.0543932,0.705024,0.64558,0.148323,0.385689,0.251047,0.286755,0.236257,0.324106,0.49846,0.635443,0.629339,0.928082,0.197918,0.268962,0.197226,0.467239,0.22944,0.496542,0.377975,0.242486,0.349807,0.716956,1.06805,0.423263,0.911622,0.124048,0.281099,0.0256534,0.633615,0.0690346,0.0124209,1.41923,0.364079,0.420511,0.111572,0.68355,0.377089,0.242227,0.275429,0.586887,0.0048652,0.246917,0.12387,0.827525,1.1648,0.804514,0.562601,0.446434,0.348406,0.0706505,0.376385,0.399529,0.483243,0.835676,0.21846,1.51946,0.441596,0.47839,0.404088,0.340503,0.904802,0.39086,0.216299,0.3681,0.490839,0.31873,0.475985,0.615165,0.161084,0.759328,0.19772,0.00796778,0.140827,0.91903,0.154062,0.626054,0.305079,0.514048,0.698687,0.863933,0.364702,0.222409,0.450719,0.66511,0.166515,0.563221,1.39703,0.678365,0.692985,0.81669,0.420713,1.36399,0.168444,0.776656,1.61314,1.21607,0.741657,0.635967,0.480173,0.341918,0.192136,0.875921,1.45545,0.406714,0.616486,0.0212532,0.00728883,0.563563,0.250074,0.648756,0.940968,0.294363,0.0641085,0.115044,0.0993076,0.740521,1.34939,0.419845,0.101015,0.354946,0.678077,0.134701,0.225998,0.000348233
}}
}}

Revision as of 14:13, 26 November 2012


Full id: C450_Eosinophils_Basophils_CD14_Neutrophils_CD14CD16_Peripheral_immature



Phase1 CAGE Peaks

Hg19::chr12:124876522..124876535,-p@chr12:124876522..124876535
-
Hg19::chr12:6248326..6248349,+p@chr12:6248326..6248349
+
Hg19::chr12:68726405..68726424,+p1@AK125933
Hg19::chr12:90256830..90256843,+p@chr12:90256830..90256843
+
Hg19::chr14:75735777..75735796,+p@chr14:75735777..75735796
+
Hg19::chr15:102182198..102182220,-p@chr15:102182198..102182220
-
Hg19::chr15:70013853..70013886,-p@chr15:70013853..70013886
-
Hg19::chr17:10055364..10055380,-p@chr17:10055364..10055380
-
Hg19::chr17:518487..518500,-p@chr17:518487..518500
-
Hg19::chr18:74774284..74774295,-p@chr18:74774284..74774295
-
Hg19::chr18:74774299..74774343,-p@chr18:74774299..74774343
-
Hg19::chr18:74775300..74775343,-p@chr18:74775300..74775343
-
Hg19::chr18:74777707..74777722,-p@chr18:74777707..74777722
-
Hg19::chr18:74826697..74826728,+p@chr18:74826697..74826728
+
Hg19::chr18:74826780..74826808,+p@chr18:74826780..74826808
+
Hg19::chr18:74843295..74843307,-p@chr18:74843295..74843307
-
Hg19::chr18:74843519..74843533,+p@chr18:74843519..74843533
+
Hg19::chr1:234977970..234977991,+p@chr1:234977970..234977991
+
Hg19::chr2:157188594..157188608,+p@chr2:157188594..157188608
+
Hg19::chr3:158520366..158520377,-p@chr3:158520366..158520377
-
Hg19::chr8:37595079..37595155,-p1@ENST00000330539
p1@uc003xkb.1
Hg19::chrX:154256125..154256129,-p@chrX:154256125..154256129
-


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 monocyte4.12e-10542
CD14-positive, CD16-negative classical monocyte4.12e-10542
myeloid leukocyte3.62e-9772
defensive cell1.91e-9048
phagocyte1.91e-9048
granulocyte monocyte progenitor cell9.16e-8067
leukocyte2.19e-78136
macrophage dendritic cell progenitor9.94e-7861
myeloid lineage restricted progenitor cell4.29e-7466
monopoietic cell2.40e-7359
monocyte2.40e-7359
monoblast2.40e-7359
promonocyte2.40e-7359
myeloid cell2.23e-65108
common myeloid progenitor2.23e-65108
hematopoietic stem cell1.68e-62168
angioblastic mesenchymal cell1.68e-62168
hematopoietic cell1.63e-58177
hematopoietic lineage restricted progenitor cell2.69e-57120
nongranular leukocyte4.97e-56115
hematopoietic oligopotent progenitor cell3.03e-55161
hematopoietic multipotent progenitor cell3.03e-55161
stuff accumulating cell1.78e-4487
intermediate monocyte4.73e-259
CD14-positive, CD16-positive monocyte4.73e-259
granulocyte1.54e-228
mesenchymal cell3.81e-21354
connective tissue cell2.04e-20361
motile cell7.39e-18386
blood cell6.20e-1611
multi fate stem cell9.89e-15427
stem cell1.72e-14441
somatic stem cell2.67e-14433
basophil1.28e-093
neutrophil2.70e-093
non-classical monocyte2.78e-093
CD14-low, CD16-positive monocyte2.78e-093
single nucleate cell1.28e-083
mononuclear cell1.28e-083
natural killer cell7.06e-083
pro-NK cell7.06e-083
eosinophil5.03e-072
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.85e-7498
blood island4.85e-7498
bone marrow6.24e-7276
hemolymphoid system6.92e-66108
bone element9.39e-6682
immune system1.98e-6193
skeletal element8.70e-5990
skeletal system1.24e-51100
lateral plate mesoderm2.39e-28203
musculoskeletal system9.21e-26167
connective tissue2.00e-19371
mesoderm5.67e-14315
mesoderm-derived structure5.67e-14315
presumptive mesoderm5.67e-14315


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)

{{{tfbs_overrepresentation_jaspar}}}



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#1053866.643036852446450.0002017924440377120.00239706563499256
BCL11A#5333556.447603432637970.0008654585595952050.00645856566670694
IRF4#366254.980571065169120.002710389575557860.0148882541882758
MAX#414982.346383821457140.01378982480437180.0485126659057427
MEF2A#420565.111790248084740.0008177710503483180.00623000880642848
NFKB1#479092.245116855352020.01109493267881160.040806580998817
PAX5#507992.728458626390930.002952719530386470.0157424613320758
SPI1#6688145.220933141787191.94204115573741e-081.38921120728808e-06



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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