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MCL coexpression mm9:223: Difference between revisions

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|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
|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
|tfbs_overrepresentation_jaspar=MA0003.1;0.0031842,MA0004.1;0.049219,MA0006.1;0.142703,MA0007.1;1.05784,MA0009.1;0.295418,MA0014.1;0.252909,MA0017.1;0.0674365,MA0019.1;0.985353,MA0024.1;0.263595,MA0025.1;0.48174,MA0027.1;1.83212,MA0028.1;0.0119309,MA0029.1;0.693412,MA0030.1;0.252855,MA0031.1;0.228273,MA0038.1;1.18463,MA0040.1;0.30473,MA0041.1;1.1929,MA0042.1;2.00359,MA0043.1;0.369607,MA0046.1;0.32239,MA0048.1;0.309389,MA0050.1;1.27775,MA0051.1;0.367015,MA0052.1;0.310775,MA0055.1;0.428665,MA0056.1;0,MA0057.1;0.950472,MA0058.1;0.0230527,MA0059.1;0.0257761,MA0060.1;0.00323147,MA0061.1;0.344993,MA0063.1;0,MA0066.1;0.104478,MA0067.1;0.577859,MA0068.1;0.0495813,MA0069.1;0.31103,MA0070.1;1.48722,MA0071.1;0.22507,MA0072.1;0.297449,MA0073.1;6.63008,MA0074.1;0.0876075,MA0076.1;0.0175818,MA0077.1;0.281511,MA0078.1;0.131891,MA0081.1;0.128121,MA0083.1;0.368979,MA0084.1;0.878418,MA0087.1;0.335323,MA0088.1;0.300577,MA0089.1;0,MA0090.1;0.151401,MA0091.1;2.17726,MA0092.1;0.151694,MA0093.1;0.0131328,MA0095.1;0,MA0098.1;0,MA0100.1;0.0824768,MA0101.1;0.0278729,MA0103.1;0.374336,MA0105.1;0.326272,MA0106.1;0.136153,MA0107.1;0.183235,MA0108.2;0.185867,MA0109.1;0,MA0111.1;0.668933,MA0113.1;0.383985,MA0114.1;0.338492,MA0115.1;0.371824,MA0116.1;0.757283,MA0117.1;0.346488,MA0119.1;0.280579,MA0122.1;0.950245,MA0124.1;0.531337,MA0125.1;0.468049,MA0130.1;0,MA0131.1;0.168986,MA0132.1;0,MA0133.1;0,MA0135.1;0.398744,MA0136.1;0.320131,MA0139.1;0.720364,MA0140.1;0.993018,MA0141.1;0.220335,MA0142.1;0.218511,MA0143.1;0.129679,MA0144.1;0.551496,MA0145.1;0.236529,MA0146.1;0.0610007,MA0147.1;0.0345488,MA0148.1;0.0547891,MA0149.1;0.0292146,MA0062.2;0.00559468,MA0035.2;0.28663,MA0039.2;0.000265488,MA0138.2;1.52213,MA0002.2;0.516387,MA0137.2;0.019155,MA0104.2;0.0156277,MA0047.2;0.354114,MA0112.2;0.00764599,MA0065.2;0.151502,MA0150.1;0.169655,MA0151.1;0,MA0152.1;0.354256,MA0153.1;0.412245,MA0154.1;0.299987,MA0155.1;0.433488,MA0156.1;0.0791428,MA0157.1;0.197497,MA0158.1;0,MA0159.1;0.642156,MA0160.1;0.0558568,MA0161.1;0,MA0162.1;0.00363264,MA0163.1;0.236693,MA0164.1;0.320592,MA0080.2;0.184454,MA0018.2;0.101591,MA0099.2;0.483832,MA0079.2;0.0525982,MA0102.2;0.928086,MA0258.1;0.0041076,MA0259.1;0.030276,MA0442.1;0
}}
}}

Revision as of 11:23, 23 January 2013


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)
MA0003.10.0031842
MA0004.10.049219
MA0006.10.142703
MA0007.11.05784
MA0009.10.295418
MA0014.10.252909
MA0017.10.0674365
MA0019.10.985353
MA0024.10.263595
MA0025.10.48174
MA0027.11.83212
MA0028.10.0119309
MA0029.10.693412
MA0030.10.252855
MA0031.10.228273
MA0038.11.18463
MA0040.10.30473
MA0041.11.1929
MA0042.12.00359
MA0043.10.369607
MA0046.10.32239
MA0048.10.309389
MA0050.11.27775
MA0051.10.367015
MA0052.10.310775
MA0055.10.428665
MA0056.10
MA0057.10.950472
MA0058.10.0230527
MA0059.10.0257761
MA0060.10.00323147
MA0061.10.344993
MA0063.10
MA0066.10.104478
MA0067.10.577859
MA0068.10.0495813
MA0069.10.31103
MA0070.11.48722
MA0071.10.22507
MA0072.10.297449
MA0073.16.63008
MA0074.10.0876075
MA0076.10.0175818
MA0077.10.281511
MA0078.10.131891
MA0081.10.128121
MA0083.10.368979
MA0084.10.878418
MA0087.10.335323
MA0088.10.300577
MA0089.10
MA0090.10.151401
MA0091.12.17726
MA0092.10.151694
MA0093.10.0131328
MA0095.10
MA0098.10
MA0100.10.0824768
MA0101.10.0278729
MA0103.10.374336
MA0105.10.326272
MA0106.10.136153
MA0107.10.183235
MA0108.20.185867
MA0109.10
MA0111.10.668933
MA0113.10.383985
MA0114.10.338492
MA0115.10.371824
MA0116.10.757283
MA0117.10.346488
MA0119.10.280579
MA0122.10.950245
MA0124.10.531337
MA0125.10.468049
MA0130.10
MA0131.10.168986
MA0132.10
MA0133.10
MA0135.10.398744
MA0136.10.320131
MA0139.10.720364
MA0140.10.993018
MA0141.10.220335
MA0142.10.218511
MA0143.10.129679
MA0144.10.551496
MA0145.10.236529
MA0146.10.0610007
MA0147.10.0345488
MA0148.10.0547891
MA0149.10.0292146
MA0062.20.00559468
MA0035.20.28663
MA0039.20.000265488
MA0138.21.52213
MA0002.20.516387
MA0137.20.019155
MA0104.20.0156277
MA0047.20.354114
MA0112.20.00764599
MA0065.20.151502
MA0150.10.169655
MA0151.10
MA0152.10.354256
MA0153.10.412245
MA0154.10.299987
MA0155.10.433488
MA0156.10.0791428
MA0157.10.197497
MA0158.10
MA0159.10.642156
MA0160.10.0558568
MA0161.10
MA0162.10.00363264
MA0163.10.236693
MA0164.10.320592
MA0080.20.184454
MA0018.20.101591
MA0099.20.483832
MA0079.20.0525982
MA0102.20.928086
MA0258.10.0041076
MA0259.10.030276
MA0442.10
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