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MCL coexpression mm9:223: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.91e-14!54;UBERON:0002780!5.40e-14!39;UBERON:0001890!5.40e-14!39;UBERON:0006240!5.40e-14!39;UBERON:0003080!1.29e-13!40;UBERON:0003528!2.58e-12!29;UBERON:0002791!2.58e-12!29;UBERON:0001893!2.58e-12!29;UBERON:0002616!1.10e-11!46;UBERON:0000955!2.07e-11!47;UBERON:0006238!2.07e-11!47;UBERON:0003056!6.79e-11!49;UBERON:0002020!2.20e-10!34;UBERON:0001017!2.69e-10!73;UBERON:0001049!3.40e-10!52;UBERON:0005068!3.40e-10!52;UBERON:0006241!3.40e-10!52;UBERON:0007135!3.40e-10!52;UBERON:0001016!5.56e-10!75;UBERON:0000956!8.53e-10!21;UBERON:0001869!8.53e-10!21;UBERON:0000203!8.53e-10!21;UBERON:0004684!3.75e-09!3;UBERON:0002275!3.75e-09!3;UBERON:0002619!1.37e-08!17;UBERON:0002346!4.75e-08!64;UBERON:0003075!4.75e-08!64;UBERON:0007284!4.75e-08!64;UBERON:0004121!1.51e-07!95;UBERON:0000924!1.51e-07!95;UBERON:0006601!1.51e-07!95;UBERON:0001851!1.83e-07!1;UBERON:0005889!1.83e-07!1;UBERON:0000470!1.83e-07!1;UBERON:0010371!6.72e-07!73
|ontology_enrichment_uberon=UBERON:0000073!1.91e-14!54;UBERON:0002780!5.40e-14!39;UBERON:0001890!5.40e-14!39;UBERON:0006240!5.40e-14!39;UBERON:0003080!1.29e-13!40;UBERON:0003528!2.58e-12!29;UBERON:0002791!2.58e-12!29;UBERON:0001893!2.58e-12!29;UBERON:0002616!1.10e-11!46;UBERON:0000955!2.07e-11!47;UBERON:0006238!2.07e-11!47;UBERON:0003056!6.79e-11!49;UBERON:0002020!2.20e-10!34;UBERON:0001017!2.69e-10!73;UBERON:0001049!3.40e-10!52;UBERON:0005068!3.40e-10!52;UBERON:0006241!3.40e-10!52;UBERON:0007135!3.40e-10!52;UBERON:0001016!5.56e-10!75;UBERON:0000956!8.53e-10!21;UBERON:0001869!8.53e-10!21;UBERON:0000203!8.53e-10!21;UBERON:0004684!3.75e-09!3;UBERON:0002275!3.75e-09!3;UBERON:0002619!1.37e-08!17;UBERON:0002346!4.75e-08!64;UBERON:0003075!4.75e-08!64;UBERON:0007284!4.75e-08!64;UBERON:0004121!1.51e-07!95;UBERON:0000924!1.51e-07!95;UBERON:0006601!1.51e-07!95;UBERON:0001851!1.83e-07!1;UBERON:0005889!1.83e-07!1;UBERON:0000470!1.83e-07!1;UBERON:0010371!6.72e-07!73
|tfbs_overrepresentation_for_novel_motifs=0.948729,0.578747,0.289038,0.184237,0.264575,0.4403,0.304022,0.742854,0.371383,0.458532,0.251079,0.604,1.00609,0.0965462,0.299782,0,0.206232,0.671438,0.0846527,0.682411,0.437988,0.718764,0.0961199,0.452706,0.553802,0.355231,0.612662,0.221799,0.185917,0.56829,0.206496,0.75737,0.661993,0.118152,0.0548669,0.242823,0.106531,0.284709,0.18583,0.640046,0.0439705,0.464231,0.0515187,0.150649,0.411154,0.693362,0.474583,0.5146,0.602157,0.616127,0.567781,0.123845,0.527908,0.384277,0.398303,0.328639,0.961502,0.576361,0.564474,0.326019,0.261673,0.404392,0.25,0.187777,0.343074,0.213975,0.51212,0.827693,0.716761,0.69152,0.258099,0.35937,0.44867,0.425631,0.0595445,0.893666,0.0209887,0.458108,0.69643,1.06875,1.70929,0.217702,0.4024,0.186895,0.333764,0.0283954,15.2389,0.260516,0.159613,0.981395,0.572773,0.337596,0.778619,1.78952,0.178828,0.453698,0.195348,0.783298,0.156877,1.60667,0.398611,0.275851,0.370402,0.568694,0.194641,0.211579,0.234223,0.506275,1.49481,0.021358,0.921343,0.371815,1.07417,0.257104,0.578983,0.252742,0.104333,0.419435,0.207083,0.387481,1.92701,1.58333,1.74188,0.456803,0.627117,0.252149,0.314276,0.28043,0.510817,0.0504481,0.35702,0.176884,0.485565,0.70465,0.5981,0.00131543,0.038545,0.0588404,0.554766,1.33894,0.950969,0.516174,0.752045,0.283669,0.190514,0.212546,0.479133,1.30006,0.99092,0.0468061,0.268613,0.0915413,0.385533,0.159342,1.15938,0.452379,0.124379,0.326255,0.141466,0.0384637,0.563096,0.333107,0.252462,0.317802,0.188422,0.335503,0.223736,0.0846945,0.693491
}}
}}

Revision as of 18:00, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126624834..126624846,+p@chr10:126624834..126624846
+
Mm9::chr10:4978253..4978267,+p33@Syne1
Mm9::chr11:56826249..56826287,+p8@Gria1
Mm9::chr11:5966399..5966414,-p11@Camk2b
Mm9::chr11:70500716..70500752,-p@chr11:70500716..70500752
-
Mm9::chr14:76651282..76651293,+p1@uc007urg.1
Mm9::chr14:76651298..76651301,+p3@uc007urg.1
Mm9::chr16:43072279..43072285,+p@chr16:43072279..43072285
+
Mm9::chr16:43072307..43072322,+p@chr16:43072307..43072322
+
Mm9::chr16:43072335..43072346,+p@chr16:43072335..43072346
+
Mm9::chr16:7217754..7217764,+p@chr16:7217754..7217764
+
Mm9::chr16:7217777..7217805,+p@chr16:7217777..7217805
+
Mm9::chr16:7217808..7217817,+p@chr16:7217808..7217817
+
Mm9::chr16:7217821..7217826,+p@chr16:7217821..7217826
+
Mm9::chr17:14386891..14386904,+p@chr17:14386891..14386904
+
Mm9::chr18:74130501..74130519,-p@chr18:74130501..74130519
-
Mm9::chr1:122237146..122237157,+p3@C1ql2
Mm9::chr1:130215797..130215815,-p@chr1:130215797..130215815
-
Mm9::chr1:156731136..156731149,-p@chr1:156731136..156731149
-
Mm9::chr1:37157454..37157461,+p@chr1:37157454..37157461
+
Mm9::chr2:104032678..104032720,-p@chr2:104032678..104032720
-
Mm9::chr2:31701445..31701472,-p1@Fibcd1
Mm9::chr2:80421620..80421636,-p9@Nckap1
Mm9::chr3:57921037..57921051,+p@chr3:57921037..57921051
+
Mm9::chr3:82351958..82351976,-p1@Npy2r
Mm9::chr3:82352013..82352024,-p2@Npy2r
Mm9::chr4:128795953..128795960,-p@chr4:128795953..128795960
-
Mm9::chr4:128795970..128795976,-p@chr4:128795970..128795976
-
Mm9::chr4:128799296..128799307,-p8@Hpca
Mm9::chr5:135039704..135039724,-p@chr5:135039704..135039724
-
Mm9::chr5:142817288..142817300,+p@chr5:142817288..142817300
+
Mm9::chr5:24565435..24565445,-p@chr5:24565435..24565445
-
Mm9::chr6:65768303..65768312,+p@chr6:65768303..65768312
+
Mm9::chr7:109720010..109720019,+p@chr7:109720010..109720019
+
Mm9::chr7:143045785..143045805,+p1@uc009ken.1
Mm9::chr7:90880911..90880947,-p14@Il16
Mm9::chr8:79423672..79423727,+p2@Nr3c2
Mm9::chr8:79423751..79423763,+p7@Nr3c2
Mm9::chr9:104469025..104469036,+p4@Cpne4


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:0051179localization0.0353914425026023
GO:0045175basal protein localization0.0353914425026023
GO:0030950establishment and/or maintenance of actin cytoskeleton polarity0.0353914425026023
GO:0032879regulation of localization0.0353914425026023
GO:0030952establishment and/or maintenance of cytoskeleton polarity0.0353914425026023
GO:0032880regulation of protein localization0.0353914425026023
GO:0007509mesoderm migration0.0423930149218979
GO:0008078mesodermal cell migration0.0423930149218979
GO:0007354zygotic determination of anterior/posterior axis, embryo0.0423930149218979
GO:0007616long-term memory0.0423930149218979
GO:0006883cellular sodium ion homeostasis0.0423930149218979
GO:0055078sodium ion homeostasis0.0423930149218979
GO:0031623receptor internalization0.0423930149218979
GO:0048570notochord morphogenesis0.0423930149218979
GO:0048617embryonic foregut morphogenesis0.0423930149218979
GO:0010172embryonic body morphogenesis0.0423930149218979
GO:0007440foregut morphogenesis0.0423930149218979
GO:0001601peptide YY receptor activity0.0423930149218979
GO:0000578embryonic axis specification0.0423930149218979
GO:0008595determination of anterior/posterior axis, embryo0.0423930149218979
GO:0010171body morphogenesis0.0423930149218979
GO:0007351tripartite regional subdivision0.0423930149218979
GO:0007350blastoderm segmentation0.0423930149218979
GO:0005954calcium- and calmodulin-dependent protein kinase complex0.0423930149218979
GO:0048611embryonic ectodermal gut development0.0423930149218979
GO:0048613embryonic ectodermal gut morphogenesis0.0423930149218979
GO:0050920regulation of chemotaxis0.0423930149218979
GO:0050926regulation of positive chemotaxis0.0423930149218979
GO:0030004cellular monovalent inorganic cation homeostasis0.0423930149218979
GO:0050921positive regulation of chemotaxis0.0423930149218979
GO:0030903notochord development0.0423930149218979
GO:0050927positive regulation of positive chemotaxis0.0423930149218979
GO:0055067monovalent inorganic cation homeostasis0.0423930149218979
GO:0050930induction of positive chemotaxis0.0423930149218979
GO:0045176apical protein localization0.0423930149218979
GO:0042074cell migration involved in gastrulation0.0434669182047715
GO:0050821protein stabilization0.0434669182047715
GO:0048558embryonic gut morphogenesis0.0434669182047715
GO:0050918positive chemotaxis0.0434669182047715
GO:0048340paraxial mesoderm morphogenesis0.0443380607181023
GO:0031647regulation of protein stability0.0443380607181023
GO:0048557embryonic digestive tract morphogenesis0.0443380607181023
GO:0008105asymmetric protein localization0.0443380607181023
GO:0007439ectodermal gut development0.0470607998849367
GO:0048567ectodermal gut morphogenesis0.0470607998849367
GO:0048547gut morphogenesis0.0495491070566289
GO:0009948anterior/posterior axis specification0.0495491070566289



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
raphe nuclei neuron3.75e-093

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.91e-1454
regional part of forebrain5.40e-1439
forebrain5.40e-1439
future forebrain5.40e-1439
anterior neural tube1.29e-1340
brain grey matter2.58e-1229
regional part of telencephalon2.58e-1229
telencephalon2.58e-1229
regional part of brain1.10e-1146
brain2.07e-1147
future brain2.07e-1147
pre-chordal neural plate6.79e-1149
gray matter2.20e-1034
central nervous system2.69e-1073
neural tube3.40e-1052
neural rod3.40e-1052
future spinal cord3.40e-1052
neural keel3.40e-1052
nervous system5.56e-1075
cerebral cortex8.53e-1021
cerebral hemisphere8.53e-1021
pallium8.53e-1021
raphe nuclei3.75e-093
reticular formation3.75e-093
regional part of cerebral cortex1.37e-0817
neurectoderm4.75e-0864
neural plate4.75e-0864
presumptive neural plate4.75e-0864
ectoderm-derived structure1.51e-0795
ectoderm1.51e-0795
presumptive ectoderm1.51e-0795
cortex1.83e-071
zygote cortex1.83e-071
cell part1.83e-071
ecto-epithelium6.72e-0773


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}}}

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