Personal tools

MCL coexpression mm9:937: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0010314!2.25e-32!92;UBERON:0002346!1.87e-24!64;UBERON:0003075!1.87e-24!64;UBERON:0007284!1.87e-24!64;UBERON:0000073!1.47e-22!54;UBERON:0010371!2.96e-21!73;UBERON:0001049!3.03e-21!52;UBERON:0005068!3.03e-21!52;UBERON:0006241!3.03e-21!52;UBERON:0007135!3.03e-21!52;UBERON:0001017!3.27e-21!73;UBERON:0001016!3.66e-21!75;UBERON:0004121!7.02e-21!95;UBERON:0000924!7.02e-21!95;UBERON:0006601!7.02e-21!95;UBERON:0003056!9.49e-20!49;UBERON:0000955!2.50e-19!47;UBERON:0006238!2.50e-19!47;UBERON:0002616!1.15e-18!46;UBERON:0003080!4.38e-17!40;UBERON:0004111!1.35e-16!122;UBERON:0002780!2.13e-16!39;UBERON:0001890!2.13e-16!39;UBERON:0006240!2.13e-16!39;UBERON:0000025!6.06e-16!114;UBERON:0002020!2.07e-13!34;UBERON:0003528!9.97e-12!29;UBERON:0002791!9.97e-12!29;UBERON:0001893!9.97e-12!29;UBERON:0000468!3.63e-09!333;UBERON:0000956!1.73e-08!21;UBERON:0001869!1.73e-08!21;UBERON:0000203!1.73e-08!21;UBERON:0002619!1.16e-07!17;UBERON:0000922!3.53e-07!320;UBERON:0002021!4.67e-07!10;UBERON:0000411!4.67e-07!10;UBERON:0001950!4.67e-07!10;UBERON:0003103!9.04e-07!43
|ontology_enrichment_uberon=UBERON:0010314!2.25e-32!92;UBERON:0002346!1.87e-24!64;UBERON:0003075!1.87e-24!64;UBERON:0007284!1.87e-24!64;UBERON:0000073!1.47e-22!54;UBERON:0010371!2.96e-21!73;UBERON:0001049!3.03e-21!52;UBERON:0005068!3.03e-21!52;UBERON:0006241!3.03e-21!52;UBERON:0007135!3.03e-21!52;UBERON:0001017!3.27e-21!73;UBERON:0001016!3.66e-21!75;UBERON:0004121!7.02e-21!95;UBERON:0000924!7.02e-21!95;UBERON:0006601!7.02e-21!95;UBERON:0003056!9.49e-20!49;UBERON:0000955!2.50e-19!47;UBERON:0006238!2.50e-19!47;UBERON:0002616!1.15e-18!46;UBERON:0003080!4.38e-17!40;UBERON:0004111!1.35e-16!122;UBERON:0002780!2.13e-16!39;UBERON:0001890!2.13e-16!39;UBERON:0006240!2.13e-16!39;UBERON:0000025!6.06e-16!114;UBERON:0002020!2.07e-13!34;UBERON:0003528!9.97e-12!29;UBERON:0002791!9.97e-12!29;UBERON:0001893!9.97e-12!29;UBERON:0000468!3.63e-09!333;UBERON:0000956!1.73e-08!21;UBERON:0001869!1.73e-08!21;UBERON:0000203!1.73e-08!21;UBERON:0002619!1.16e-07!17;UBERON:0000922!3.53e-07!320;UBERON:0002021!4.67e-07!10;UBERON:0000411!4.67e-07!10;UBERON:0001950!4.67e-07!10;UBERON:0003103!9.04e-07!43
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.96259,0.434198,0.720982,0.448401,0.538088,0.173246,0.181564,0.687027,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.485665,0.549359,0.717658,0.978733,0.577606,0.153291,0.469052,0.818708,0.376624,1.15331,0.843667,1.29258,0.839887,0.757987,1.25792,0.242032,0.522578,1.1836,0.195877,0.256422,0.460258,0.450632,0.27776,0.403938,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,1.64913,0.527912,0.236196,1.03623,0.433216,0.813951,0.42492,1.56933,0.806481,0.336166,0.530481,0.759925,0.612313,0.501608,0.920903,0.789543,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,1.12826,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.887702,1.00333,0.96962,0.337254,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,1.35892,0.950857,0.427043,1.10792,0.570914,1.23736,3.57892,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.381863,0.203102,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.2562,0.524587,0.331912
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.96259,0.434198,0.720982,0.448401,0.538088,0.173246,0.181564,0.687027,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.485665,0.549359,0.717658,0.978733,0.577606,0.153291,0.469052,0.818708,0.376624,1.15331,0.843667,1.29258,0.839887,0.757987,1.25792,0.242032,0.522578,1.1836,0.195877,0.256422,0.460258,0.450632,0.27776,0.403938,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,1.64913,0.527912,0.236196,1.03623,0.433216,0.813951,0.42492,1.56933,0.806481,0.336166,0.530481,0.759925,0.612313,0.501608,0.920903,0.789543,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,1.12826,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.887702,1.00333,0.96962,0.337254,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,1.35892,0.950857,0.427043,1.10792,0.570914,1.23736,3.57892,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.381863,0.203102,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.2562,0.524587,0.331912
|tfbs_overrepresentation_jaspar=MA0003.1;0.602903,MA0004.1;1.10905,MA0006.1;0.747445,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.162935,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.685543,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.117901,MA0056.1;0,MA0057.1;0.643187,MA0058.1;1.62198,MA0059.1;0.353484,MA0060.1;1.08928,MA0061.1;0.638933,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.0216016,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.49616,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;1.43515,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;1.06639,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;1.36991,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.527241,MA0146.1;0.636109,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.426733,MA0035.2;0.524137,MA0039.2;0.812684,MA0138.2;1.61926,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.2464,MA0065.2;0.902537,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.230918,MA0163.1;0.991519,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;1.00617,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:33, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:73187080..73187134,+p1@Jkamp
Mm9::chr18:35862762..35862787,-p2@Dnajc18
Mm9::chr19:60937293..60937365,-p1@Sfxn4
Mm9::chr7:52894108..52894158,-p1@uc009gwj.1
Mm9::chr9:4376533..4376600,+p1@8430410K20Rik
Mm9::chrX:100551803..100551827,+p3@Chic1
Mm9::chrX:133242515..133242579,+p1@Tceal1
Mm9::chrX:68745767..68745833,-p1@Cd99l2


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

no results for this coexpression

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
electrically responsive cell4.44e-0739
electrically active cell4.44e-0739
neuron7.71e-0733
neuronal stem cell7.71e-0733
neuroblast7.71e-0733
electrically signaling cell7.71e-0733

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest2.25e-3292
neurectoderm1.87e-2464
neural plate1.87e-2464
presumptive neural plate1.87e-2464
regional part of nervous system1.47e-2254
ecto-epithelium2.96e-2173
neural tube3.03e-2152
neural rod3.03e-2152
future spinal cord3.03e-2152
neural keel3.03e-2152
central nervous system3.27e-2173
nervous system3.66e-2175
ectoderm-derived structure7.02e-2195
ectoderm7.02e-2195
presumptive ectoderm7.02e-2195
pre-chordal neural plate9.49e-2049
brain2.50e-1947
future brain2.50e-1947
regional part of brain1.15e-1846
anterior neural tube4.38e-1740
anatomical conduit1.35e-16122
regional part of forebrain2.13e-1639
forebrain2.13e-1639
future forebrain2.13e-1639
tube6.06e-16114
gray matter2.07e-1334
brain grey matter9.97e-1229
regional part of telencephalon9.97e-1229
telencephalon9.97e-1229
multi-cellular organism3.63e-09333
cerebral cortex1.73e-0821
cerebral hemisphere1.73e-0821
pallium1.73e-0821
regional part of cerebral cortex1.16e-0717
embryo3.53e-07320
occipital lobe4.67e-0710
visual cortex4.67e-0710
neocortex4.67e-0710
compound organ9.04e-0743


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)
MA0003.10.602903
MA0004.11.10905
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.162935
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.117901
MA0056.10
MA0057.10.643187
MA0058.11.62198
MA0059.10.353484
MA0060.11.08928
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.0216016
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.11.43515
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.11.36991
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.636109
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.426733
MA0035.20.524137
MA0039.20.812684
MA0138.21.61926
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.2464
MA0065.20.902537
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.991519
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.21.00617
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:937&oldid=2574332"