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MCL coexpression mm9:2326: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!5.74e-21!95;UBERON:0000924!5.74e-21!95;UBERON:0006601!5.74e-21!95;UBERON:0001016!3.13e-20!75;UBERON:0001017!3.36e-20!73;UBERON:0010371!4.03e-15!73;UBERON:0000073!1.46e-14!54;UBERON:0001049!1.23e-13!52;UBERON:0005068!1.23e-13!52;UBERON:0006241!1.23e-13!52;UBERON:0007135!1.23e-13!52;UBERON:0002020!3.32e-13!34;UBERON:0002346!1.88e-12!64;UBERON:0003075!1.88e-12!64;UBERON:0007284!1.88e-12!64;UBERON:0000955!7.02e-12!47;UBERON:0006238!7.02e-12!47;UBERON:0003528!1.91e-11!29;UBERON:0002791!1.91e-11!29;UBERON:0001893!1.91e-11!29;UBERON:0002616!2.42e-11!46;UBERON:0003080!6.71e-10!40;UBERON:0002780!1.88e-09!39;UBERON:0001890!1.88e-09!39;UBERON:0006240!1.88e-09!39;UBERON:0000956!3.62e-09!21;UBERON:0001869!3.62e-09!21;UBERON:0000203!3.62e-09!21;UBERON:0002619!7.67e-09!17;UBERON:0003056!4.58e-08!49;UBERON:0002021!6.15e-08!10;UBERON:0000411!6.15e-08!10;UBERON:0001950!6.15e-08!10;UBERON:0000991!4.90e-07!18;UBERON:0005564!4.90e-07!18;UBERON:0004176!7.64e-07!17;UBERON:0009196!7.64e-07!17;UBERON:0009117!7.64e-07!17
|ontology_enrichment_uberon=UBERON:0004121!5.74e-21!95;UBERON:0000924!5.74e-21!95;UBERON:0006601!5.74e-21!95;UBERON:0001016!3.13e-20!75;UBERON:0001017!3.36e-20!73;UBERON:0010371!4.03e-15!73;UBERON:0000073!1.46e-14!54;UBERON:0001049!1.23e-13!52;UBERON:0005068!1.23e-13!52;UBERON:0006241!1.23e-13!52;UBERON:0007135!1.23e-13!52;UBERON:0002020!3.32e-13!34;UBERON:0002346!1.88e-12!64;UBERON:0003075!1.88e-12!64;UBERON:0007284!1.88e-12!64;UBERON:0000955!7.02e-12!47;UBERON:0006238!7.02e-12!47;UBERON:0003528!1.91e-11!29;UBERON:0002791!1.91e-11!29;UBERON:0001893!1.91e-11!29;UBERON:0002616!2.42e-11!46;UBERON:0003080!6.71e-10!40;UBERON:0002780!1.88e-09!39;UBERON:0001890!1.88e-09!39;UBERON:0006240!1.88e-09!39;UBERON:0000956!3.62e-09!21;UBERON:0001869!3.62e-09!21;UBERON:0000203!3.62e-09!21;UBERON:0002619!7.67e-09!17;UBERON:0003056!4.58e-08!49;UBERON:0002021!6.15e-08!10;UBERON:0000411!6.15e-08!10;UBERON:0001950!6.15e-08!10;UBERON:0000991!4.90e-07!18;UBERON:0005564!4.90e-07!18;UBERON:0004176!7.64e-07!17;UBERON:0009196!7.64e-07!17;UBERON:0009117!7.64e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.641384,2.54893,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,1.72258,1.91144,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,4.51897,0.790816,0.711848,1.12823,1.18815,0.318879,0.503207,2.75365,2.02937,0.786577,0.434783,1.82692,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.882473,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,1.44172,0.377213,1.12016,1.32691,2.36634,0.834514,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,0.129654,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.731844,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,2.39857,0.633483,1.25851,0.576517,0.7614,1.51002,1.1991,0.442329,0.692434,1.02384,1.15537,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.79777,2.32792,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,0.589293
}}
}}

Revision as of 21:15, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr2:119625278..119625308,+p1@Tyro3
Mm9::chr2:119625310..119625328,+p4@Tyro3
Mm9::chr5:123229287..123229443,-p1@Camkk2
Mm9::chr5:135516995..135517035,+p2@Stx1a


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:0019855calcium channel inhibitor activity0.0268556468270756
GO:0008200ion channel inhibitor activity0.0268556468270756
GO:0016248channel inhibitor activity0.0268556468270756
GO:0005246calcium channel regulator activity0.0268556468270756
GO:0004683calmodulin-dependent protein kinase activity0.0268556468270756
GO:0016247channel regulator activity0.0268556468270756
GO:0015457auxiliary transport protein activity0.0268556468270756
GO:0000149SNARE binding0.0268556468270756
GO:0004672protein kinase activity0.0268556468270756
GO:0017156calcium ion-dependent exocytosis0.0282399074109683
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0298844870419492
GO:0016301kinase activity0.0447116880677966
GO:0006836neurotransmitter transport0.0499513795386572
GO:0016772transferase activity, transferring phosphorus-containing groups0.0499513795386572



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
ectodermal cell1.33e-0944
neurectodermal cell1.33e-0944
neuron1.82e-0933
neuronal stem cell1.82e-0933
neuroblast1.82e-0933
electrically signaling cell1.82e-0933
neural cell2.16e-0943
non-terminally differentiated cell1.95e-0849
electrically responsive cell3.07e-0839
electrically active cell3.07e-0839

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure5.74e-2195
ectoderm5.74e-2195
presumptive ectoderm5.74e-2195
nervous system3.13e-2075
central nervous system3.36e-2073
ecto-epithelium4.03e-1573
regional part of nervous system1.46e-1454
neural tube1.23e-1352
neural rod1.23e-1352
future spinal cord1.23e-1352
neural keel1.23e-1352
gray matter3.32e-1334
neurectoderm1.88e-1264
neural plate1.88e-1264
presumptive neural plate1.88e-1264
brain7.02e-1247
future brain7.02e-1247
brain grey matter1.91e-1129
regional part of telencephalon1.91e-1129
telencephalon1.91e-1129
regional part of brain2.42e-1146
anterior neural tube6.71e-1040
regional part of forebrain1.88e-0939
forebrain1.88e-0939
future forebrain1.88e-0939
cerebral cortex3.62e-0921
cerebral hemisphere3.62e-0921
pallium3.62e-0921
regional part of cerebral cortex7.67e-0917
pre-chordal neural plate4.58e-0849
occipital lobe6.15e-0810
visual cortex6.15e-0810
neocortex6.15e-0810
gonad4.90e-0718
gonad primordium4.90e-0718
external genitalia7.64e-0717
indifferent external genitalia7.64e-0717
indifferent gonad7.64e-0717


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}}}