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Coexpression cluster:C2196: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286663152283957!BCL11A#53335;3:21.2770913277053:0.000170483911460614:0.00208101557141597!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199413191740086!FOS#2353;3:6.7484664816708:0.00503245277631794:0.02345625632641!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112822487501441!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249142770214804
|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286663152283957!BCL11A#53335;3:21.2770913277053:0.000170483911460614:0.00208101557141597!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199413191740086!FOS#2353;3:6.7484664816708:0.00503245277631794:0.02345625632641!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112822487501441!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249142770214804
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.911389,0.49475,0.598278,0.491074,0.740899,0.463978,0.971732,0.493145,0.66492,0.539378,0.53106,0.314427,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.353274,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498
}}
}}

Revision as of 15:21, 26 November 2012


Full id: C2196_Basophils_Eosinophils_CD14_Peripheral_Neutrophils_immature_CD14CD16



Phase1 CAGE Peaks

Hg19::chr12:124875522..124875536,+p@chr12:124875522..124875536
+
Hg19::chr15:63795718..63795739,+p@chr15:63795718..63795739
+
Hg19::chr15:90931911..90931927,-p@chr15:90931911..90931927
-
Hg19::chr18:74777638..74777673,+p@chr18:74777638..74777673
+


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
leukocyte5.90e-61136
hematopoietic stem cell4.84e-55168
angioblastic mesenchymal cell4.84e-55168
myeloid leukocyte2.16e-5372
hematopoietic cell2.25e-50177
hematopoietic oligopotent progenitor cell7.40e-50161
hematopoietic multipotent progenitor cell7.40e-50161
classical monocyte2.64e-4942
CD14-positive, CD16-negative classical monocyte2.64e-4942
hematopoietic lineage restricted progenitor cell2.31e-47120
granulocyte monocyte progenitor cell1.21e-4667
nongranular leukocyte2.77e-46115
defensive cell4.70e-4548
phagocyte4.70e-4548
macrophage dendritic cell progenitor5.30e-4361
myeloid cell6.41e-43108
common myeloid progenitor6.41e-43108
myeloid lineage restricted progenitor cell1.30e-4166
monopoietic cell7.43e-4159
monocyte7.43e-4159
monoblast7.43e-4159
promonocyte7.43e-4159
mesenchymal cell1.16e-27354
connective tissue cell2.56e-26361
motile cell2.77e-23386
stuff accumulating cell5.68e-1887
multi fate stem cell1.54e-17427
stem cell2.53e-17441
somatic stem cell3.30e-17433
intermediate monocyte1.92e-129
CD14-positive, CD16-positive monocyte1.92e-129
granulocyte2.39e-118
native cell4.64e-09722
somatic cell3.21e-08588
lymphoid lineage restricted progenitor cell5.92e-0852
lymphocyte1.15e-0753
common lymphoid progenitor1.15e-0753
blood cell1.39e-0711
nucleate cell3.96e-0755
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.39e-4898
blood island5.39e-4898
bone marrow7.08e-4276
hemolymphoid system4.32e-41108
bone element3.27e-3782
immune system8.78e-3493
skeletal element5.44e-3290
skeletal system9.07e-28100
connective tissue3.89e-25371
lateral plate mesoderm2.88e-18203
mesoderm6.51e-11315
mesoderm-derived structure6.51e-11315
presumptive mesoderm6.51e-11315
musculoskeletal system1.55e-10167
blood6.93e-0815
haemolymphatic fluid6.93e-0815
organism substance6.93e-0815


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#10538318.26835134422770.0002681660105721290.00286663152283957
BCL11A#53335321.27709132770530.0001704839114606140.00208101557141597
EBF1#187948.9064668465690.00015887907472010.00199413191740086
FOS#235336.74846648167080.005032452776317940.02345625632641
JUN#372539.384621894252250.001918994502030470.0112822487501441
SPI1#668848.204323508522730.000220661881527680.00249142770214804



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.