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Coexpression cluster:C303: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;6:3.65367026884555:0.0055224974640936:0.0250027792895991!IRF4#3662;7:3.83503972018022:0.00203047490418992:0.0117949145402242
|tf_chipseq_enrich=BATF#10538;6:3.65367026884555:0.0055224974640936:0.0250027792895991!IRF4#3662;7:3.83503972018022:0.00203047490418992:0.0117949145402242
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|tfbs_overrepresentation_for_novel_motifs=0.098819,0.476858,0.0934085,0.225967,0.173355,0.486601,0.313269,0.388534,0.813458,0.170765,0.0517073,0.369089,0.794475,0.621607,0.570244,0.964502,0.22071,1.23074,0.283316,1.34732,0.232711,0.0578144,0.215784,1.56567,0.305958,0.399598,0.31286,0.466844,0.177466,0.0819437,0.386187,0.24564,1.02128,0.586555,0.0470026,0.532885,0.00890084,0.488923,0.60484,0.03927,1.00844,0.356507,0.132387,1.19181,0.678724,0.520504,0.0947455,0.0481165,0.490254,0.177638,0.13465,0.100268,0.355426,0.300601,0.419703,0.0903335,0.360115,0.0761472,0.0817919,0.0757301,0.274483,0.0958427,0.229006,0.202595,0.340398,0.533977,0.49328,1.92606,1.2468,0.674502,0.143174,0.0562828,0.000985334,0.418072,0.00650564,0.0192725,0.814677,0.560338,0.665592,0.295621,0.172796,0.201905,0.339944,0.240282,0.376745,0.0162748,0.00829703,0.373002,0.455643,0.91755,0.573976,0.355545,0.257337,0.775576,0.174338,0.0958374,0.278915,0.784165,0.151759,1.60885,1.19857,0.253382,0.774942,0.634805,0.173898,0.050191,0.212683,0.29483,0.129173,0.0566971,0.101681,0.281754,0.22435,0.054941,1.31787,0.694297,0.280621,0.383971,0.179492,0.540661,0.411341,0.885808,0.221175,0.718879,0.629528,0.56149,0.0913382,0.260851,0.446285,0.0329348,0.937137,2.57824,0.458238,0.350217,0.585312,0.0292852,1.03756,0.21407,0.548138,1.35786,0.96741,0.515888,1.06277,0.778331,0.174963,0.540265,1.52654,1.2021,0.35056,0.0264613,0.062165,0.00214436,0.937795,0.0452507,0.653266,0.70233,0.140053,0.529201,1.27687,0.024919,0.514845,0.905988,0.235753,0.263993,0.543455,0.691694,0.00383484,1.07337,0.0545292
}}
}}

Revision as of 14:06, 26 November 2012


Full id: C303_CD14_Basophils_Peripheral_Eosinophils_CD14CD16_Neutrophils_Whole



Phase1 CAGE Peaks

Hg19::chr10:135073029..135073042,+p@chr10:135073029..135073042
+
Hg19::chr11:64163297..64163310,-p1@ENST00000457725
Hg19::chr11:65220998..65221001,+p@chr11:65220998..65221001
+
Hg19::chr11:66888450..66888468,-p@chr11:66888450..66888468
-
Hg19::chr12:69747591..69747611,-p1@ENST00000548626
Hg19::chr13:99922932..99922946,-p@chr13:99922932..99922946
-
Hg19::chr13:99930136..99930140,+p1@AF339795
Hg19::chr13:99932682..99932704,+p@chr13:99932682..99932704
+
Hg19::chr13:99932706..99932716,+p@chr13:99932706..99932716
+
Hg19::chr13:99934075..99934096,-p@chr13:99934075..99934096
-
Hg19::chr14:75754624..75754635,+p@chr14:75754624..75754635
+
Hg19::chr17:7024749..7024764,-p@chr17:7024749..7024764
-
Hg19::chr17:7077590..7077615,-p@chr17:7077590..7077615
-
Hg19::chr17:7077620..7077625,-p@chr17:7077620..7077625
-
Hg19::chr17:72524949..72524975,+p@chr17:72524949..72524975
+
Hg19::chr17:72774120..72774160,-p@chr17:72774120..72774160
-
Hg19::chr17:72776484..72776500,+p@chr17:72776484..72776500
+
Hg19::chr17:72776516..72776526,+p@chr17:72776516..72776526
+
Hg19::chr17:81060279..81060283,-p@chr17:81060279..81060283
-
Hg19::chr17:81101323..81101338,+p@chr17:81101323..81101338
+
Hg19::chr17:81103271..81103285,-p@chr17:81103271..81103285
-
Hg19::chr17:81103526..81103542,+p@chr17:81103526..81103542
+
Hg19::chr17:81147900..81147911,+p@chr17:81147900..81147911
+
Hg19::chr1:10057123..10057149,+p3@RBP7
Hg19::chr22:37976067..37976079,-p3@LGALS2
Hg19::chr2:230162106..230162117,-p@chr2:230162106..230162117
-
Hg19::chr2:230162122..230162143,-p@chr2:230162122..230162143
-
Hg19::chr5:139631154..139631161,-p@chr5:139631154..139631161
-
Hg19::chr5:139725653..139725678,-p@chr5:139725653..139725678
-
Hg19::chr6:11537600..11537651,-p@chr6:11537600..11537651
-
Hg19::chr6:163826254..163826261,+p@chr6:163826254..163826261
+
Hg19::chr6:163827012..163827025,-p@chr6:163827012..163827025
-
Hg19::chr7:2774708..2774727,-p@chr7:2774708..2774727
-
Hg19::chr7:2797828..2797848,-p@chr7:2797828..2797848
-
Hg19::chr8:48273366..48273391,+p3@KIAA0146
Hg19::chr8:48273416..48273419,+p15@KIAA0146
Hg19::chr8:48282088..48282092,-p@chr8:48282088..48282092
-
Hg19::chr8:48513543..48513562,+p@chr8:48513543..48513562
+
Hg19::chr8:48540690..48540694,+p@chr8:48540690..48540694
+
Hg19::chr9:27701766..27701787,-p@chr9:27701766..27701787
-


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:0019841retinol binding0.00425250120614753
GO:0016918retinal binding0.00425250120614753
GO:0005501retinoid binding0.00425250120614753
GO:0019840isoprenoid binding0.00425250120614753
GO:0005625soluble fraction0.0407202229474492
GO:0019842vitamin binding0.0407202229474492
GO:0005529sugar binding0.0493596312651508



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 monocyte3.31e-14142
CD14-positive, CD16-negative classical monocyte3.31e-14142
defensive cell1.50e-12248
phagocyte1.50e-12248
monopoietic cell2.00e-9659
monocyte2.00e-9659
monoblast2.00e-9659
promonocyte2.00e-9659
macrophage dendritic cell progenitor4.71e-9361
myeloid leukocyte5.84e-9272
myeloid lineage restricted progenitor cell1.67e-8566
granulocyte monocyte progenitor cell3.97e-8467
stuff accumulating cell5.64e-6487
nongranular leukocyte1.27e-60115
myeloid cell8.24e-59108
common myeloid progenitor8.24e-59108
leukocyte1.43e-58136
hematopoietic lineage restricted progenitor cell7.45e-49120
hematopoietic stem cell7.82e-46168
angioblastic mesenchymal cell7.82e-46168
hematopoietic cell4.49e-43177
hematopoietic oligopotent progenitor cell5.64e-41161
hematopoietic multipotent progenitor cell5.64e-41161
intermediate monocyte1.14e-399
CD14-positive, CD16-positive monocyte1.14e-399
mesenchymal cell3.70e-17354
connective tissue cell1.19e-16361
motile cell7.27e-15386
basophil3.45e-143
single nucleate cell3.77e-143
mononuclear cell3.77e-143
non-classical monocyte9.89e-143
CD14-low, CD16-positive monocyte9.89e-143
multi fate stem cell1.12e-12427
somatic stem cell2.24e-12433
stem cell5.52e-12441
circulating cell2.77e-076
Uber Anatomy
Ontology termp-valuen
bone marrow2.42e-7376
bone element1.88e-6782
hematopoietic system1.38e-6598
blood island1.38e-6598
skeletal element8.37e-6190
hemolymphoid system8.52e-59108
immune system1.33e-5893
skeletal system5.67e-54100
musculoskeletal system3.68e-29167
lateral plate mesoderm1.93e-27203
connective tissue5.84e-16371
mesoderm1.16e-15315
mesoderm-derived structure1.16e-15315
presumptive mesoderm1.16e-15315


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#1053863.653670268845550.00552249746409360.0250027792895991
IRF4#366273.835039720180220.002030474904189920.0117949145402242



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

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