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Coexpression cluster:C622: Difference between revisions

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|tf_chipseq_enrich=NFKB1#4790;7:2.74403171209692:0.00686995190103442:0.0290965126968707!POU2F2#5452;5:3.25218716347947:0.0136235155601946:0.0480733297831254
|tf_chipseq_enrich=NFKB1#4790;7:2.74403171209692:0.00686995190103442:0.0290965126968707!POU2F2#5452;5:3.25218716347947:0.0136235155601946:0.0480733297831254
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|tfbs_overrepresentation_for_novel_motifs=0.18943,0.1536,0.183956,0.806989,0.153879,0.296522,0.360887,0.270053,0.0771434,0.586318,0.271739,1.03072,0.20272,0.925865,0.907585,0.506197,0.560096,0.752071,0.0612687,0.403976,0.541421,0.121811,0.290113,0.150321,0.218509,1.07436,0.0456804,0.288329,0.472898,0.152963,0.706977,0.594213,0.320109,0.205943,0.130292,0.139795,0.12818,0.29748,0.363308,0.881025,0.806754,0.241157,0.495734,0.151865,0.664236,0.206995,0.361827,0.262957,0.456684,0.473123,0.431291,0.372023,0.780607,0.666176,0.811691,0.353512,0.15913,0.325599,0.152817,0.324748,0.632472,0.363871,0.564331,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,0.652781,0.585859,0.103789,0.80977,0.196336,0.402042,0.368241,0.519091,0.581542,0.61268,0.227702,0.533593,0.37913,0.274429,0.760489,0.0478103,1.7691,0.146775,0.454557,1.35556,0.98765,0.734737,0.609873,0.331798,0.154399,0.71683,0.476274,0.649779,1.16091,0.552868,0.73791,0.6046,0.644537,0.563483,0.492631,0.268065,0.548871,0.348037,0.218314,0.142849,0.19228,0.641937,0.531469,1.3989,0.940917,0.12714,0.0638634,0.704759,0.500972,0.102878,0.801818,0.452379,0.294241,1.78671,1.04884,0.519787,0.355419,0.614537,0.842806,0.719563,0.735394,0.256408,0.856671,0.386057,1.00021,0.588214,0.249339,0.288795,0.95886,1.80749,1.40745,0.922589,0.356906,0.646464,0.494226,0.318465,0.47912,1.64894,1.2469,0.0991414,0.712398,0.0473433,0.735758,0.541074,0.363452,1.12781,0.440071,0.443316,0.218554,0.196611,0.921409,0.718143,0.580811,0.199028,0.508869,0.378443,0.0919059,0.35974,0.0337609
}}
}}

Revision as of 14:21, 26 November 2012


Full id: C622_CD19_CD14_immature_Peripheral_Neutrophils_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr11:6633799..6633813,-p11@TAF10
Hg19::chr16:19222406..19222410,-p@chr16:19222406..19222410
-
Hg19::chr1:1005339..1005350,-p@chr1:1005339..1005350
-
Hg19::chr1:179050670..179050709,+p3@TOR3A
Hg19::chr1:226298353..226298372,-p@chr1:226298353..226298372
-
Hg19::chr2:33701603..33701615,-p@chr2:33701603..33701615
-
Hg19::chr2:88905814..88905819,-p@chr2:88905814..88905819
-
Hg19::chr2:88909458..88909464,-p1@AK129635
Hg19::chr4:103680719..103680723,-p@chr4:103680719..103680723
-
Hg19::chr5:149790235..149790248,-p@chr5:149790235..149790248
-
Hg19::chr6:14127098..14127123,+p@chr6:14127098..14127123
+
Hg19::chr6:14127175..14127200,+p@chr6:14127175..14127200
+
Hg19::chr6:167507740..167507764,+p@chr6:167507740..167507764
+
Hg19::chr8:102218459..102218472,-p8@ZNF706


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:0051085chaperone cofactor-dependent protein folding0.0334245397562372
GO:0006458'de novo' protein folding0.0334245397562372
GO:0051084'de novo' posttranslational protein folding0.0334245397562372
GO:0005669transcription factor TFIID complex0.0469838878480247



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
leukocyte2.07e-85136
nongranular leukocyte2.01e-67115
hematopoietic stem cell4.28e-67168
angioblastic mesenchymal cell4.28e-67168
hematopoietic cell2.30e-66177
hematopoietic lineage restricted progenitor cell3.97e-66120
hematopoietic oligopotent progenitor cell1.80e-58161
hematopoietic multipotent progenitor cell1.80e-58161
classical monocyte2.34e-4942
CD14-positive, CD16-negative classical monocyte2.34e-4942
defensive cell7.99e-4248
phagocyte7.99e-4248
myeloid leukocyte1.26e-4172
granulocyte monocyte progenitor cell5.80e-4167
macrophage dendritic cell progenitor8.42e-3961
myeloid lineage restricted progenitor cell6.00e-3766
monopoietic cell1.63e-3559
monocyte1.63e-3559
monoblast1.63e-3559
promonocyte1.63e-3559
myeloid cell4.93e-31108
common myeloid progenitor4.93e-31108
lymphocyte5.98e-2553
common lymphoid progenitor5.98e-2553
nucleate cell1.01e-2355
lymphoid lineage restricted progenitor cell1.04e-2352
mesenchymal cell1.28e-20354
connective tissue cell8.26e-20361
lymphocyte of B lineage1.17e-1924
pro-B cell1.17e-1924
stuff accumulating cell2.00e-1887
motile cell5.73e-17386
stem cell7.95e-14441
multi fate stem cell1.61e-13427
dendritic cell1.95e-1310
somatic stem cell4.79e-13433
B cell9.86e-1114
intermediate monocyte1.00e-109
CD14-positive, CD16-positive monocyte1.00e-109
Langerhans cell4.31e-105
conventional dendritic cell5.13e-108
circulating cell6.71e-096
natural killer cell6.23e-083
pro-NK cell6.23e-083
single nucleate cell1.52e-073
mononuclear cell1.52e-073
basophil2.65e-073
plasmacytoid dendritic cell3.55e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.81e-4198
blood island7.81e-4198
hemolymphoid system2.67e-37108
bone marrow1.09e-3676
immune system1.37e-3593
bone element4.19e-3382
skeletal element4.49e-2990
skeletal system5.92e-25100
connective tissue1.04e-18371
lateral plate mesoderm1.83e-12203
musculoskeletal system2.23e-10167
Disease
Ontology termp-valuen
lymphoma4.49e-0810


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
NFKB1#479072.744031712096920.006869951901034420.0290965126968707
POU2F2#545253.252187163479470.01362351556019460.0480733297831254



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.