Personal tools

MCL coexpression mm9:1791: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 6: Line 6:
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!1.20e-34!64;UBERON:0003075!1.20e-34!64;UBERON:0007284!1.20e-34!64;UBERON:0004121!5.12e-34!95;UBERON:0000924!5.12e-34!95;UBERON:0006601!5.12e-34!95;UBERON:0001016!6.23e-33!75;UBERON:0001017!4.35e-32!73;UBERON:0003056!1.09e-30!49;UBERON:0000073!1.51e-30!54;UBERON:0010371!8.58e-30!73;UBERON:0001049!1.93e-28!52;UBERON:0005068!1.93e-28!52;UBERON:0006241!1.93e-28!52;UBERON:0007135!1.93e-28!52;UBERON:0000955!1.78e-25!47;UBERON:0006238!1.78e-25!47;UBERON:0002616!1.51e-24!46;UBERON:0003080!3.30e-24!40;UBERON:0002780!1.33e-23!39;UBERON:0001890!1.33e-23!39;UBERON:0006240!1.33e-23!39;UBERON:0002020!1.64e-23!34;UBERON:0010314!1.51e-21!92;UBERON:0003528!2.40e-20!29;UBERON:0002791!2.40e-20!29;UBERON:0001893!2.40e-20!29;UBERON:0000956!1.82e-15!21;UBERON:0001869!1.82e-15!21;UBERON:0000203!1.82e-15!21;UBERON:0002619!2.34e-12!17;UBERON:0002021!1.79e-08!10;UBERON:0000411!1.79e-08!10;UBERON:0001950!1.79e-08!10;UBERON:0000020!3.30e-07!12;UBERON:0001032!3.30e-07!12;UBERON:0004456!3.30e-07!12;UBERON:0000970!4.48e-07!9;UBERON:0000019!4.48e-07!9;UBERON:0000047!4.48e-07!9;UBERON:0010312!4.48e-07!9;UBERON:0004088!4.48e-07!9;UBERON:0002104!4.48e-07!9;UBERON:0001456!4.48e-07!9;UBERON:0003072!4.48e-07!9;UBERON:0004128!4.48e-07!9;UBERON:0003071!4.48e-07!9
|ontology_enrichment_uberon=UBERON:0002346!1.20e-34!64;UBERON:0003075!1.20e-34!64;UBERON:0007284!1.20e-34!64;UBERON:0004121!5.12e-34!95;UBERON:0000924!5.12e-34!95;UBERON:0006601!5.12e-34!95;UBERON:0001016!6.23e-33!75;UBERON:0001017!4.35e-32!73;UBERON:0003056!1.09e-30!49;UBERON:0000073!1.51e-30!54;UBERON:0010371!8.58e-30!73;UBERON:0001049!1.93e-28!52;UBERON:0005068!1.93e-28!52;UBERON:0006241!1.93e-28!52;UBERON:0007135!1.93e-28!52;UBERON:0000955!1.78e-25!47;UBERON:0006238!1.78e-25!47;UBERON:0002616!1.51e-24!46;UBERON:0003080!3.30e-24!40;UBERON:0002780!1.33e-23!39;UBERON:0001890!1.33e-23!39;UBERON:0006240!1.33e-23!39;UBERON:0002020!1.64e-23!34;UBERON:0010314!1.51e-21!92;UBERON:0003528!2.40e-20!29;UBERON:0002791!2.40e-20!29;UBERON:0001893!2.40e-20!29;UBERON:0000956!1.82e-15!21;UBERON:0001869!1.82e-15!21;UBERON:0000203!1.82e-15!21;UBERON:0002619!2.34e-12!17;UBERON:0002021!1.79e-08!10;UBERON:0000411!1.79e-08!10;UBERON:0001950!1.79e-08!10;UBERON:0000020!3.30e-07!12;UBERON:0001032!3.30e-07!12;UBERON:0004456!3.30e-07!12;UBERON:0000970!4.48e-07!9;UBERON:0000019!4.48e-07!9;UBERON:0000047!4.48e-07!9;UBERON:0010312!4.48e-07!9;UBERON:0004088!4.48e-07!9;UBERON:0002104!4.48e-07!9;UBERON:0001456!4.48e-07!9;UBERON:0003072!4.48e-07!9;UBERON:0004128!4.48e-07!9;UBERON:0003071!4.48e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.02681,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,3.93412,0.702872,0.812978,0.728641,0.424775,0,0.930881,0.397593,0.283802,1.0421,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,0.456327,1.87618,0.626183,1.03545,1.02297,0.704734,0.425309,0.20704,2.66119,1.66799,0.360612,0.328675,1.03785,0.631725,0.134724,0.426986,0.84962,2.45957,0.847828,1.58288,0.746467,0.459555,0.912738,0.786094,1.17664,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,2.08407,1.76944,0.943088,1.33705,1.68977,1.00999,1.54147,1.26875,0.30684,20.9395,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,1.23692,0.308173,0.948899,0.794502,0.293164,1.1148,0.272382,0.618102,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,24.908,0.3366,1.46478,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,21.8367,3.1533,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,5.18669,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,2.2879,0.724289,1.04166,1.33551,0.416189,1.14546,1.45154,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,15.295,1.18223,1.62749,0.749664,1.26545,0.787153,0.438007,0.555203,1.39093,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
}}
}}

Revision as of 20:26, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr3:26230826..26230839,-p6@Nlgn1
Mm9::chr5:84846323..84846334,-p3@Epha5
Mm9::chr5:84846349..84846362,-p2@Epha5
Mm9::chr5:84846393..84846414,-p1@Epha5
Mm9::chr5:84846420..84846425,-p4@Epha5


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:0016080synaptic vesicle targeting0.0240970418475486
GO:0006903vesicle targeting0.0240970418475486
GO:0042043neurexin binding0.0240970418475486
GO:0016079synaptic vesicle exocytosis0.0240970418475486
GO:0051650establishment of vesicle localization0.0240970418475486
GO:0051648vesicle localization0.0240970418475486
GO:0005003ephrin receptor activity0.0240970418475486
GO:0007416synaptogenesis0.0270995143755786
GO:0051656establishment of organelle localization0.0270995143755786
GO:0048489synaptic vesicle transport0.0270995143755786
GO:0051640organelle localization0.0270995143755786
GO:0045664regulation of neuron differentiation0.0270995143755786
GO:0050808synapse organization and biogenesis0.0407460835267628
GO:0007269neurotransmitter secretion0.0438465372469897
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0481280481196195
GO:0045055regulated secretory pathway0.0481280481196195



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>


Uber Anatomy
Ontology termp-valuen
neurectoderm1.20e-3464
neural plate1.20e-3464
presumptive neural plate1.20e-3464
ectoderm-derived structure5.12e-3495
ectoderm5.12e-3495
presumptive ectoderm5.12e-3495
nervous system6.23e-3375
central nervous system4.35e-3273
pre-chordal neural plate1.09e-3049
regional part of nervous system1.51e-3054
ecto-epithelium8.58e-3073
neural tube1.93e-2852
neural rod1.93e-2852
future spinal cord1.93e-2852
neural keel1.93e-2852
brain1.78e-2547
future brain1.78e-2547
regional part of brain1.51e-2446
anterior neural tube3.30e-2440
regional part of forebrain1.33e-2339
forebrain1.33e-2339
future forebrain1.33e-2339
gray matter1.64e-2334
structure with developmental contribution from neural crest1.51e-2192
brain grey matter2.40e-2029
regional part of telencephalon2.40e-2029
telencephalon2.40e-2029
cerebral cortex1.82e-1521
cerebral hemisphere1.82e-1521
pallium1.82e-1521
regional part of cerebral cortex2.34e-1217
occipital lobe1.79e-0810
visual cortex1.79e-0810
neocortex1.79e-0810
sense organ3.30e-0712
sensory system3.30e-0712
entire sense organ system3.30e-0712
eye4.48e-079
camera-type eye4.48e-079
simple eye4.48e-079
immature eye4.48e-079
ocular region4.48e-079
visual system4.48e-079
face4.48e-079
optic cup4.48e-079
optic vesicle4.48e-079
eye primordium4.48e-079


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}}}