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MCL coexpression mm9:576: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.63e-18!46;UBERON:0002193!7.35e-15!48;UBERON:0002405!7.35e-15!48;UBERON:0002390!5.35e-14!45;UBERON:0003061!5.35e-14!45;UBERON:0004177!3.41e-10!29;UBERON:0005057!3.41e-10!29;UBERON:0002370!7.56e-09!23;UBERON:0000974!7.56e-09!23;UBERON:0004807!7.56e-09!23;UBERON:0005058!7.56e-09!23;UBERON:0003351!7.56e-09!23;UBERON:0009113!7.56e-09!23;UBERON:0003295!7.56e-09!23;UBERON:0009722!7.56e-09!23;UBERON:0005562!7.56e-09!23;UBERON:0007690!7.56e-09!23;UBERON:0006562!2.03e-08!24;UBERON:0003408!2.03e-08!24;UBERON:0001557!2.03e-08!24;UBERON:0001042!2.03e-08!24;UBERON:0008814!2.03e-08!24;UBERON:0009145!2.03e-08!24;UBERON:0000077!4.23e-08!35;UBERON:0000072!2.55e-07!27
|ontology_enrichment_uberon=UBERON:0002384!1.63e-18!46;UBERON:0002193!7.35e-15!48;UBERON:0002405!7.35e-15!48;UBERON:0002390!5.35e-14!45;UBERON:0003061!5.35e-14!45;UBERON:0004177!3.41e-10!29;UBERON:0005057!3.41e-10!29;UBERON:0002370!7.56e-09!23;UBERON:0000974!7.56e-09!23;UBERON:0004807!7.56e-09!23;UBERON:0005058!7.56e-09!23;UBERON:0003351!7.56e-09!23;UBERON:0009113!7.56e-09!23;UBERON:0003295!7.56e-09!23;UBERON:0009722!7.56e-09!23;UBERON:0005562!7.56e-09!23;UBERON:0007690!7.56e-09!23;UBERON:0006562!2.03e-08!24;UBERON:0003408!2.03e-08!24;UBERON:0001557!2.03e-08!24;UBERON:0001042!2.03e-08!24;UBERON:0008814!2.03e-08!24;UBERON:0009145!2.03e-08!24;UBERON:0000077!4.23e-08!35;UBERON:0000072!2.55e-07!27
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.341626,0.223558,0.279403,0.848472,0.792702,0.370193,0.566731,0.59395,0.282547,0.331725,0.35958,0.0780266,0.381063,0.898708,0,0.557619,0.824658,0.524522,0.119642,0.194751,0.197405,0.38026,0.427399,0.64994,0.405649,0.501183,0.309422,0.171781,0.384773,0.297405,0.653099,0.131928,0.0552712,0.151158,0.195932,0.125578,0.356403,0.725176,0.0929685,0.42301,0.301802,0.347242,0.152251,0.0508111,0.743728,0.48361,0.322976,0.742531,0.173974,0.541299,0.429887,0.366754,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,0.090369,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.984639,0.0186364,0.838198,0.0571922,0.0517462,0.447182,0.473159,0.617814,1.09058,0.989763,0.573903,0.437131,0.932192,0.72691,0.00415894,1.1039,0.170021,0.488122,1.44275,1.0064,0.731688,0.665283,0.866261,0.108477,0.661488,0.264364,0.667958,0.483845,0.597503,0.125632,1.5718,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,0.201775,0.196131,0.238877,0.773781,0.19888,0.336214,1.01331,0.134943,0.00714903,1.41039,0.558838,0.123076,0.843435,1.27363,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,0.145259,0.755703,0.273302,0.907893,0.399614,1.03449,0.193774,0.700863,0.303003,0.986296,1.80931,1.41113,2.16948,1.07314,0.66306,1.32358,0.302189,0.486482,1.76978,0.253405,0.140226,0.173337,0.0139939,0.790393,0.331601,1.03101,0.869538,0.430798,0.159498,0.242603,0.251242,0.995609,0.726089,0.621734,0.237049,0.531751,0.392164,0.39393,0.941787,0.00980506
}}
}}

Revision as of 18:34, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr16:45225058..45225071,+p@chr16:45225058..45225071
+
Mm9::chr16:45225090..45225101,+p@chr16:45225090..45225101
+
Mm9::chr17:34115798..34115805,-p2@H2-K2
Mm9::chr17:88981299..88981314,+p@chr17:88981299..88981314
+
Mm9::chr1:54642295..54642307,-p@chr1:54642295..54642307
-
Mm9::chr2:58011604..58011622,-p@chr2:58011604..58011622
-
Mm9::chr2:58012598..58012610,+p@chr2:58012598..58012610
+
Mm9::chr2:58012625..58012639,+p@chr2:58012625..58012639
+
Mm9::chr2:58013483..58013521,-p3@Cytip
Mm9::chr5:112702785..112702808,-p@chr5:112702785..112702808
-
Mm9::chr5:139643031..139643037,+p4@Heatr2
Mm9::chr9:32423847..32423875,+p@chr9:32423847..32423875
+
Mm9::chr9:32562231..32562235,+p@chr9:32562231..32562235
+


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


GO IDGO nameFDR corrected p-value
GO:0030155regulation of cell adhesion0.0193118939352435
GO:0005938cell cortex0.0193118939352435



Relative expression of the co-expression cluster over median <br>Analyst:





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
lymphoid lineage restricted progenitor cell6.49e-3012
hematopoietic lineage restricted progenitor cell1.42e-2925
hematopoietic cell2.61e-2832
hematopoietic oligopotent progenitor cell2.61e-2832
hematopoietic stem cell2.61e-2832
angioblastic mesenchymal cell2.61e-2832
hematopoietic multipotent progenitor cell2.61e-2832
lymphocyte1.90e-2713
common lymphoid progenitor1.90e-2713
T cell6.56e-2711
pro-T cell6.56e-2711
nucleate cell6.82e-2216
mature alpha-beta T cell1.58e-219
alpha-beta T cell1.58e-219
immature T cell1.58e-219
mature T cell1.58e-219
immature alpha-beta T cell1.58e-219
leukocyte1.78e-2017
nongranular leukocyte1.78e-2017
CD4-positive, alpha-beta T cell1.09e-188
connective tissue cell1.63e-1846
mesenchymal cell1.63e-1846
motile cell3.39e-1554
megakaryocyte progenitor cell1.23e-136
megakaryocyte1.23e-136
thymocyte7.43e-136
double negative thymocyte7.43e-136
naive T cell7.43e-136
double-positive, alpha-beta thymocyte7.43e-136
CD4-positive, alpha-beta thymocyte7.43e-136
naive thymus-derived CD4-positive, alpha-beta T cell7.43e-136
DN4 thymocyte7.43e-136
DN1 thymic pro-T cell7.43e-136
DN2 thymocyte7.43e-136
DN3 thymocyte7.43e-136
immature single positive thymocyte7.43e-136
early T lineage precursor7.43e-136
mature CD4 single-positive thymocyte7.43e-136
resting double-positive thymocyte7.43e-136
double-positive blast7.43e-136
CD69-positive double-positive thymocyte7.43e-136
CD69-positive, CD4-positive single-positive thymocyte7.43e-136
CD4-positive, CD8-intermediate double-positive thymocyte7.43e-136
CD24-positive, CD4 single-positive thymocyte7.43e-136
megakaryocyte-erythroid progenitor cell5.67e-099
stem cell9.27e-0997
somatic stem cell1.85e-0791
multi fate stem cell1.85e-0791
common myeloid progenitor3.08e-0719


TFBS overrepresentation<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}}}