MCL coexpression mm9:1004: Difference between revisions
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{{MCL_coexpression_mm9| | 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5084131504676,0.0413232520190408,0,0,0,0.120876255993453,0,0,0,0.0194374924235553,0.0523284672130554,0.0242538736058389,0,0,0,0,0.0596387295197733,0,0.0354759961767123,0.092873634605593,0.0589368614163519,0.0195303707501796,0.0515875539845187,0.104181599639904,0,0,0,0.0243442052522616,0.0408018333703219,0,0,0,0.136412877324794,0.0456455446387725,0,0,0,0|gostat_on_MCL_coexpression=GO:0019101;female somatic sex determination;0.00169835095600723;26927!GO:0030237;female sex determination;0.00169835095600723;26927!GO:0060014;granulosa cell differentiation;0.00169835095600723;26927!GO:0018993;somatic sex determination;0.00254752643401085;26927!GO:0048048;embryonic eye morphogenesis;0.00611406344162603;26927!GO:0001541;ovarian follicle development;0.0134654968654859;26927!GO:0048562;embryonic organ morphogenesis;0.0134654968654859;26927!GO:0007530;sex determination;0.0134654968654859;26927!GO:0022601;menstrual cycle phase;0.0134654968654859;26927!GO:0022602;menstrual cycle process;0.0134654968654859;26927!GO:0008585;female gonad development;0.0134654968654859;26927!GO:0046545;development of primary female sexual characteristics;0.0134654968654859;26927!GO:0046660;female sex differentiation;0.0134654968654859;26927!GO:0048568;embryonic organ development;0.0134654968654859;26927!GO:0042698;menstrual cycle;0.0135868076480578;26927!GO:0048592;eye morphogenesis;0.0136929545828083;26927!GO:0008406;gonad development;0.0150021001113972;26927!GO:0048608;reproductive structure development;0.0150021001113972;26927!GO:0045137;development of primary sexual characteristics;0.0155533192813294;26927!GO:0048609;reproductive process in a multicellular organism;0.0169063117893447;26927!GO:0032504;multicellular organism reproduction;0.0169063117893447;26927!GO:0007548;sex differentiation;0.0169063117893447;26927!GO:0003006;reproductive developmental process;0.0190510672456463;26927!GO:0001654;eye development;0.022078562428094;26927!GO:0006917;induction of apoptosis;0.0252793007682615;26927!GO:0012502;induction of programmed cell death;0.0252793007682615;26927!GO:0043065;positive regulation of apoptosis;0.0300244186865564;26927!GO:0043068;positive regulation of programmed cell death;0.0300244186865564;26927!GO:0007423;sensory organ development;0.0326786149466219;26927!GO:0045944;positive regulation of transcription from RNA polymerase II promoter;0.0327994028378897;26927!GO:0048598;embryonic morphogenesis;0.0327994028378897;26927!GO:0022414;reproductive process;0.0327994028378897;26927!GO:0045893;positive regulation of transcription, DNA-dependent;0.0364373477834279;26927!GO:0045941;positive regulation of transcription;0.0417794335177779;26927!GO:0045935;positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0417794335177779;26927!GO:0031325;positive regulation of cellular metabolic process;0.0484030022462061;26927!GO:0009893;positive regulation of metabolic process;0.0484030022462061;26927!GO:0042981;regulation of apoptosis;0.0484030022462061;26927!GO:0043067;regulation of programmed cell death;0.0484030022462061;26927!GO:0006357;regulation of transcription from RNA polymerase II promoter;0.0484030022462061;26927!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000007!6.12e-13!8;UBERON:0003296!6.12e-13!8;UBERON:0010133!6.12e-13!8;UBERON:0003056!7.27e-13!49;UBERON:0001894!2.33e-12!10;UBERON:0006222!2.33e-12!10;UBERON:0000474!1.54e-11!9;UBERON:0002346!6.35e-11!64;UBERON:0003075!6.35e-11!64;UBERON:0007284!6.35e-11!64;UBERON:0003134!5.06e-10!8;UBERON:0003100!4.40e-09!11;UBERON:0005156!8.80e-09!26;UBERON:0000990!8.80e-09!26;UBERON:0010371!1.16e-08!73;UBERON:0000970!2.00e-08!9;UBERON:0000019!2.00e-08!9;UBERON:0000047!2.00e-08!9;UBERON:0010312!2.00e-08!9;UBERON:0004088!2.00e-08!9;UBERON:0002104!2.00e-08!9;UBERON:0001456!2.00e-08!9;UBERON:0003072!2.00e-08!9;UBERON:0004128!2.00e-08!9;UBERON:0003071!2.00e-08!9;UBERON:0003133!3.45e-08!24;UBERON:0002780!1.33e-07!39;UBERON:0001890!1.33e-07!39;UBERON:0006240!1.33e-07!39;UBERON:0002616!1.81e-07!46;UBERON:0003080!2.66e-07!40;UBERON:0000955!3.31e-07!47;UBERON:0006238!3.31e-07!47;UBERON:0001049!8.85e-07!52;UBERON:0005068!8.85e-07!52;UBERON:0006241!8.85e-07!52;UBERON:0007135!8.85e-07!52|tfbs_overrepresentation_for_novel_motifs=0.393008,0.84953,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.181564,2.55967,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.0887261,0.332107,1.26895,0.549359,0.258745,0.374936,3.53682,2.09255,0.469052,0.303071,0.118137,0.455168,0.843667,0.699026,1.35821,0.276324,0.363049,0.242032,0.522578,0.221921,0.195877,0.256422,0.460258,0.0558565,0.27776,2.25434,0.423266,0.662995,0.484612,0.0447507,0.305876,0.725127,0.604356,1.75805,0.985264,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,3.19733,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,2.49185,0.178433,0.0665967,1.03623,1.37807,1.32088,0.136938,0.651651,0.806481,0.336166,1.01677,0.759925,0.612313,1.54237,0.920903,1.15003,1.68006,0.376919,1.60318,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,1.99856,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,3.10425,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,1.30779,5.56305,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,3.53491,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,0.0553085,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.558175|tfbs_overrepresentation_jaspar=MA0003.1;1.45843,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;4.06656,MA0017.1;0.804572,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;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.0283571,MA0056.1;0,MA0057.1;1.58436,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.319589,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.082812,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.980744,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.064239,MA0089.1;0,MA0090.1;1.82869,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,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;0.415012,MA0113.1;0.598933,MA0114.1;1.18683,MA0115.1;0.969632,MA0116.1;0.27152,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;1.55504,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.900473,MA0146.1;3.23209,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;2.43328,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.18504,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;2.91306,MA0155.1;0.978338,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;0.453546,MA0161.1;0,MA0162.1;1.4435,MA0163.1;0.669601,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;10.1641,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0}} | ||
Latest revision as of 16:14, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr9:98855201..98855222,- | p@chr9:98855201..98855222 - |
| Mm9::chr9:98855692..98855710,+ | p2@Foxl2 |
| Mm9::chr9:98855721..98855732,- | p2@Foxl2os |
| Mm9::chr9:98855759..98855767,- | p3@Foxl2os |
| Mm9::chr9:98855847..98855866,+ | p3@Foxl2 |
| Mm9::chr9:98855868..98855895,+ | p1@Foxl2 |
| Mm9::chr9:98855944..98855971,+ | p4@Foxl2 |
| Mm9::chr9:98857712..98857715,- | p@chr9:98857712..98857715 - |
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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0019101 | female somatic sex determination | 0.00169835095600723 |
| GO:0030237 | female sex determination | 0.00169835095600723 |
| GO:0060014 | granulosa cell differentiation | 0.00169835095600723 |
| GO:0018993 | somatic sex determination | 0.00254752643401085 |
| GO:0048048 | embryonic eye morphogenesis | 0.00611406344162603 |
| GO:0001541 | ovarian follicle development | 0.0134654968654859 |
| GO:0048562 | embryonic organ morphogenesis | 0.0134654968654859 |
| GO:0007530 | sex determination | 0.0134654968654859 |
| GO:0022601 | menstrual cycle phase | 0.0134654968654859 |
| GO:0022602 | menstrual cycle process | 0.0134654968654859 |
| GO:0008585 | female gonad development | 0.0134654968654859 |
| GO:0046545 | development of primary female sexual characteristics | 0.0134654968654859 |
| GO:0046660 | female sex differentiation | 0.0134654968654859 |
| GO:0048568 | embryonic organ development | 0.0134654968654859 |
| GO:0042698 | menstrual cycle | 0.0135868076480578 |
| GO:0048592 | eye morphogenesis | 0.0136929545828083 |
| GO:0008406 | gonad development | 0.0150021001113972 |
| GO:0048608 | reproductive structure development | 0.0150021001113972 |
| GO:0045137 | development of primary sexual characteristics | 0.0155533192813294 |
| GO:0048609 | reproductive process in a multicellular organism | 0.0169063117893447 |
| GO:0032504 | multicellular organism reproduction | 0.0169063117893447 |
| GO:0007548 | sex differentiation | 0.0169063117893447 |
| GO:0003006 | reproductive developmental process | 0.0190510672456463 |
| GO:0001654 | eye development | 0.022078562428094 |
| GO:0006917 | induction of apoptosis | 0.0252793007682615 |
| GO:0012502 | induction of programmed cell death | 0.0252793007682615 |
| GO:0043065 | positive regulation of apoptosis | 0.0300244186865564 |
| GO:0043068 | positive regulation of programmed cell death | 0.0300244186865564 |
| GO:0007423 | sensory organ development | 0.0326786149466219 |
| GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 0.0327994028378897 |
| GO:0048598 | embryonic morphogenesis | 0.0327994028378897 |
| GO:0022414 | reproductive process | 0.0327994028378897 |
| GO:0045893 | positive regulation of transcription, DNA-dependent | 0.0364373477834279 |
| GO:0045941 | positive regulation of transcription | 0.0417794335177779 |
| GO:0045935 | positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0417794335177779 |
| GO:0031325 | positive regulation of cellular metabolic process | 0.0484030022462061 |
| GO:0009893 | positive regulation of metabolic process | 0.0484030022462061 |
| GO:0042981 | regulation of apoptosis | 0.0484030022462061 |
| GO:0043067 | regulation of programmed cell death | 0.0484030022462061 |
| GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.0484030022462061 |
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><br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| pituitary gland | 6.12e-13 | 8 |
| gland of diencephalon | 6.12e-13 | 8 |
| neuroendocrine gland | 6.12e-13 | 8 |
| pre-chordal neural plate | 7.27e-13 | 49 |
| diencephalon | 2.33e-12 | 10 |
| future diencephalon | 2.33e-12 | 10 |
| female reproductive system | 1.54e-11 | 9 |
| neurectoderm | 6.35e-11 | 64 |
| neural plate | 6.35e-11 | 64 |
| presumptive neural plate | 6.35e-11 | 64 |
| female reproductive organ | 5.06e-10 | 8 |
| female organism | 4.40e-09 | 11 |
| reproductive structure | 8.80e-09 | 26 |
| reproductive system | 8.80e-09 | 26 |
| ecto-epithelium | 1.16e-08 | 73 |
| eye | 2.00e-08 | 9 |
| camera-type eye | 2.00e-08 | 9 |
| simple eye | 2.00e-08 | 9 |
| immature eye | 2.00e-08 | 9 |
| ocular region | 2.00e-08 | 9 |
| visual system | 2.00e-08 | 9 |
| face | 2.00e-08 | 9 |
| optic cup | 2.00e-08 | 9 |
| optic vesicle | 2.00e-08 | 9 |
| eye primordium | 2.00e-08 | 9 |
| reproductive organ | 3.45e-08 | 24 |
| regional part of forebrain | 1.33e-07 | 39 |
| forebrain | 1.33e-07 | 39 |
| future forebrain | 1.33e-07 | 39 |
| regional part of brain | 1.81e-07 | 46 |
| anterior neural tube | 2.66e-07 | 40 |
| brain | 3.31e-07 | 47 |
| future brain | 3.31e-07 | 47 |
| neural tube | 8.85e-07 | 52 |
| neural rod | 8.85e-07 | 52 |
| future spinal cord | 8.85e-07 | 52 |
| neural keel | 8.85e-07 | 52 |
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) |
|---|---|
| MA0003.1 | 1.45843 |
| MA0004.1 | 0.434673 |
| MA0006.1 | 0.271714 |
| MA0007.1 | 0.419994 |
| MA0009.1 | 0.870101 |
| MA0014.1 | 4.06656 |
| MA0017.1 | 0.804572 |
| 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 | 0.102483 |
| MA0050.1 | 0.472794 |
| MA0051.1 | 0.586414 |
| MA0052.1 | 0.890676 |
| MA0055.1 | 0.0283571 |
| MA0056.1 | 0 |
| MA0057.1 | 1.58436 |
| MA0058.1 | 0.341628 |
| MA0059.1 | 0.353484 |
| MA0060.1 | 0.197678 |
| MA0061.1 | 0.224905 |
| MA0063.1 | 0 |
| MA0066.1 | 0.566617 |
| MA0067.1 | 1.21448 |
| MA0068.1 | 0.319589 |
| MA0069.1 | 0.891016 |
| MA0070.1 | 0.881319 |
| MA0071.1 | 0.471969 |
| MA0072.1 | 0.872842 |
| MA0073.1 | 0.082812 |
| MA0074.1 | 0.531046 |
| MA0076.1 | 0.315013 |
| MA0077.1 | 0.851175 |
| MA0078.1 | 0.61926 |
| MA0081.1 | 0.980744 |
| MA0083.1 | 0.96604 |
| MA0084.1 | 1.54225 |
| MA0087.1 | 0.922929 |
| MA0088.1 | 0.064239 |
| MA0089.1 | 0 |
| MA0090.1 | 1.82869 |
| MA0091.1 | 0.447561 |
| MA0092.1 | 0.401504 |
| MA0093.1 | 0.289361 |
| 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 | 0.415012 |
| MA0113.1 | 0.598933 |
| MA0114.1 | 1.18683 |
| MA0115.1 | 0.969632 |
| MA0116.1 | 0.27152 |
| 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 | 1.55504 |
| MA0140.1 | 0.519484 |
| MA0141.1 | 0.325895 |
| MA0142.1 | 0.761136 |
| MA0143.1 | 0.615203 |
| MA0144.1 | 0.225588 |
| MA0145.1 | 0.900473 |
| MA0146.1 | 3.23209 |
| MA0147.1 | 0.236889 |
| MA0148.1 | 0.450593 |
| MA0149.1 | 0.367458 |
| MA0062.2 | 0.137653 |
| MA0035.2 | 0.524137 |
| MA0039.2 | 2.43328 |
| MA0138.2 | 0.675599 |
| MA0002.2 | 0.172399 |
| MA0137.2 | 0.32312 |
| MA0104.2 | 0.18504 |
| 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 | 2.91306 |
| MA0155.1 | 0.978338 |
| MA0156.1 | 0.314185 |
| MA0157.1 | 0.729116 |
| MA0158.1 | 0 |
| MA0159.1 | 0.688775 |
| MA0160.1 | 0.453546 |
| MA0161.1 | 0 |
| MA0162.1 | 1.4435 |
| MA0163.1 | 0.669601 |
| MA0164.1 | 0.551114 |
| MA0080.2 | 0.302064 |
| MA0018.2 | 0.560731 |
| MA0099.2 | 0.669311 |
| MA0079.2 | 10.1641 |
| MA0102.2 | 1.59466 |
| MA0258.1 | 0.210437 |
| MA0259.1 | 0.227035 |
| MA0442.1 | 0 |
