MCL coexpression mm9:118: Difference between revisions
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Latest revision as of 14:43, 17 September 2013
Phase1 CAGE Peaks
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:0005515 | protein binding | 0.000732003941750997 |
GO:0050870 | positive regulation of T cell activation | 0.000732003941750997 |
GO:0045321 | leukocyte activation | 0.000856604389875852 |
GO:0042110 | T cell activation | 0.000856604389875852 |
GO:0001775 | cell activation | 0.000856604389875852 |
GO:0006417 | regulation of translation | 0.000856604389875852 |
GO:0051251 | positive regulation of lymphocyte activation | 0.000856604389875852 |
GO:0050863 | regulation of T cell activation | 0.000856604389875852 |
GO:0031326 | regulation of cellular biosynthetic process | 0.000876283834534143 |
GO:0002376 | immune system process | 0.0011136549310473 |
GO:0009889 | regulation of biosynthetic process | 0.00121499007636724 |
GO:0051239 | regulation of multicellular organismal process | 0.00149222120358652 |
GO:0051249 | regulation of lymphocyte activation | 0.0015771067843541 |
GO:0050865 | regulation of cell activation | 0.00168456114761738 |
GO:0042108 | positive regulation of cytokine biosynthetic process | 0.0020225994520369 |
GO:0046649 | lymphocyte activation | 0.00216112170926091 |
GO:0005522 | profilin binding | 0.00276394954686717 |
GO:0045727 | positive regulation of translation | 0.00331794579367454 |
GO:0031328 | positive regulation of cellular biosynthetic process | 0.00380315419863275 |
GO:0051246 | regulation of protein metabolic process | 0.00380315419863275 |
GO:0031294 | lymphocyte costimulation | 0.00380315419863275 |
GO:0031295 | T cell costimulation | 0.00380315419863275 |
GO:0045086 | positive regulation of interleukin-2 biosynthetic process | 0.00380315419863275 |
GO:0050856 | regulation of T cell receptor signaling pathway | 0.00466966713143797 |
GO:0042035 | regulation of cytokine biosynthetic process | 0.00466966713143797 |
GO:0007242 | intracellular signaling cascade | 0.00497680671866625 |
GO:0009891 | positive regulation of biosynthetic process | 0.00514494169406404 |
GO:0050854 | regulation of antigen receptor-mediated signaling pathway | 0.00611164206805233 |
GO:0042089 | cytokine biosynthetic process | 0.00692533152575002 |
GO:0042107 | cytokine metabolic process | 0.00703037073106021 |
GO:0048518 | positive regulation of biological process | 0.0070739884332495 |
GO:0045076 | regulation of interleukin-2 biosynthetic process | 0.00756353113539419 |
GO:0045621 | positive regulation of lymphocyte differentiation | 0.00908952033762646 |
GO:0042094 | interleukin-2 biosynthetic process | 0.00908952033762646 |
GO:0006405 | RNA export from nucleus | 0.00908952033762646 |
GO:0051247 | positive regulation of protein metabolic process | 0.00908952033762646 |
GO:0006955 | immune response | 0.00908952033762646 |
GO:0032623 | interleukin-2 production | 0.00908952033762646 |
GO:0032943 | mononuclear cell proliferation | 0.00908952033762646 |
GO:0048732 | gland development | 0.00908952033762646 |
GO:0046651 | lymphocyte proliferation | 0.00908952033762646 |
GO:0031349 | positive regulation of defense response | 0.00976123523726513 |
GO:0050729 | positive regulation of inflammatory response | 0.00976123523726513 |
GO:0050852 | T cell receptor signaling pathway | 0.0107173362862481 |
GO:0008624 | induction of apoptosis by extracellular signals | 0.0116962206835666 |
GO:0042113 | B cell activation | 0.0121454574214118 |
GO:0001772 | immunological synapse | 0.0123616527377006 |
GO:0031325 | positive regulation of cellular metabolic process | 0.0123616527377006 |
GO:0030097 | hemopoiesis | 0.0136179774384505 |
GO:0030098 | lymphocyte differentiation | 0.0136179774384505 |
GO:0040018 | positive regulation of multicellular organism growth | 0.0136179774384505 |
GO:0030879 | mammary gland development | 0.0136179774384505 |
GO:0009893 | positive regulation of metabolic process | 0.0138309058830415 |
GO:0050789 | regulation of biological process | 0.0138309058830415 |
GO:0045619 | regulation of lymphocyte differentiation | 0.0138309058830415 |
GO:0051168 | nuclear export | 0.0138309058830415 |
GO:0050778 | positive regulation of immune response | 0.0139510050672506 |
GO:0007165 | signal transduction | 0.0142475669200382 |
GO:0002684 | positive regulation of immune system process | 0.0143052548597772 |
GO:0001816 | cytokine production | 0.014485077860282 |
GO:0050871 | positive regulation of B cell activation | 0.0157291000176367 |
GO:0045927 | positive regulation of growth | 0.0157291000176367 |
GO:0005044 | scavenger receptor activity | 0.0157291000176367 |
GO:0048534 | hemopoietic or lymphoid organ development | 0.016193424702035 |
GO:0050851 | antigen receptor-mediated signaling pathway | 0.016193424702035 |
GO:0042102 | positive regulation of T cell proliferation | 0.016193424702035 |
GO:0050776 | regulation of immune response | 0.0176129731681724 |
GO:0003779 | actin binding | 0.0176129731681724 |
GO:0031347 | regulation of defense response | 0.0176129731681724 |
GO:0050727 | regulation of inflammatory response | 0.0176129731681724 |
GO:0002682 | regulation of immune system process | 0.0178999325386018 |
GO:0002520 | immune system development | 0.0186757732366673 |
GO:0051240 | positive regulation of multicellular organismal process | 0.0186757732366673 |
GO:0004871 | signal transducer activity | 0.0186757732366673 |
GO:0060089 | molecular transducer activity | 0.0186757732366673 |
GO:0006412 | translation | 0.0186757732366673 |
GO:0002429 | immune response-activating cell surface receptor signaling pathway | 0.0186757732366673 |
GO:0021542 | dentate gyrus development | 0.0186757732366673 |
GO:0000164 | protein phosphatase type 1 complex | 0.0186757732366673 |
GO:0030338 | CMP-N-acetylneuraminate monooxygenase activity | 0.0186757732366673 |
GO:0046831 | regulation of RNA export from nucleus | 0.0186757732366673 |
GO:0002768 | immune response-regulating cell surface receptor signaling pathway | 0.0206361137915273 |
GO:0010468 | regulation of gene expression | 0.0207823045086254 |
GO:0002521 | leukocyte differentiation | 0.0210575175617036 |
GO:0006917 | induction of apoptosis | 0.0210575175617036 |
GO:0012502 | induction of programmed cell death | 0.0210575175617036 |
GO:0002757 | immune response-activating signal transduction | 0.0210575175617036 |
GO:0050671 | positive regulation of lymphocyte proliferation | 0.0210575175617036 |
GO:0032946 | positive regulation of mononuclear cell proliferation | 0.0210575175617036 |
GO:0000792 | heterochromatin | 0.0210575175617036 |
GO:0050864 | regulation of B cell activation | 0.0218613711677571 |
GO:0007154 | cell communication | 0.0218613711677571 |
GO:0002252 | immune effector process | 0.022200941104786 |
GO:0004715 | non-membrane spanning protein tyrosine kinase activity | 0.022200941104786 |
GO:0002764 | immune response-regulating signal transduction | 0.022200941104786 |
GO:0002377 | immunoglobulin production | 0.0231260799055712 |
GO:0002440 | production of molecular mediator of immune response | 0.0240598754174787 |
GO:0031323 | regulation of cellular metabolic process | 0.0241916454060806 |
GO:0042129 | regulation of T cell proliferation | 0.0259519270168955 |
GO:0050794 | regulation of cellular process | 0.0275712176750654 |
GO:0048522 | positive regulation of cellular process | 0.0275712176750654 |
GO:0048583 | regulation of response to stimulus | 0.0276009528750531 |
GO:0046544 | development of secondary male sexual characteristics | 0.0279731342327435 |
GO:0046543 | development of secondary female sexual characteristics | 0.0279731342327435 |
GO:0046381 | CMP-N-acetylneuraminate metabolic process | 0.0279731342327435 |
GO:0042405 | nuclear inclusion body | 0.0279731342327435 |
GO:0007527 | adult somatic muscle development | 0.0279731342327435 |
GO:0016716 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen | 0.0279731342327435 |
GO:0065007 | biological regulation | 0.0279731342327435 |
GO:0019222 | regulation of metabolic process | 0.0285936106661784 |
GO:0043065 | positive regulation of apoptosis | 0.0317220006838718 |
GO:0050657 | nucleic acid transport | 0.0317220006838718 |
GO:0050658 | RNA transport | 0.0317220006838718 |
GO:0051236 | establishment of RNA localization | 0.0317220006838718 |
GO:0043068 | positive regulation of programmed cell death | 0.0321316261835247 |
GO:0006403 | RNA localization | 0.0321316261835247 |
GO:0007517 | muscle development | 0.0321316261835247 |
GO:0008092 | cytoskeletal protein binding | 0.0328064009132407 |
GO:0040014 | regulation of multicellular organism growth | 0.0328064009132407 |
GO:0032944 | regulation of mononuclear cell proliferation | 0.0334843856276656 |
GO:0050670 | regulation of lymphocyte proliferation | 0.0334843856276656 |
GO:0015931 | nucleobase, nucleoside, nucleotide and nucleic acid transport | 0.0345707701314824 |
GO:0042098 | T cell proliferation | 0.0345707701314824 |
GO:0045136 | development of secondary sexual characteristics | 0.0345707701314824 |
GO:0051283 | negative regulation of sequestering of calcium ion | 0.0345707701314824 |
GO:0051238 | sequestering of metal ion | 0.0345707701314824 |
GO:0051209 | release of sequestered calcium ion into cytosol | 0.0345707701314824 |
GO:0051208 | sequestering of calcium ion | 0.0345707701314824 |
GO:0001553 | luteinization | 0.0345707701314824 |
GO:0007525 | somatic muscle development | 0.0345707701314824 |
GO:0051282 | regulation of sequestering of calcium ion | 0.0345707701314824 |
GO:0048523 | negative regulation of cellular process | 0.0392872805480568 |
GO:0030217 | T cell differentiation | 0.0397245761498175 |
GO:0035264 | multicellular organism growth | 0.0397245761498175 |
GO:0044260 | cellular macromolecule metabolic process | 0.0401401268775371 |
GO:0010467 | gene expression | 0.0401401268775371 |
GO:0030326 | embryonic limb morphogenesis | 0.0401401268775371 |
GO:0035113 | embryonic appendage morphogenesis | 0.0401401268775371 |
GO:0042981 | regulation of apoptosis | 0.0401401268775371 |
GO:0048468 | cell development | 0.0401401268775371 |
GO:0043067 | regulation of programmed cell death | 0.0401401268775371 |
GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 0.0401401268775371 |
GO:0001779 | natural killer cell differentiation | 0.0401401268775371 |
GO:0016973 | poly(A)+ mRNA export from nucleus | 0.0401401268775371 |
GO:0045078 | positive regulation of interferon-gamma biosynthetic process | 0.0401401268775371 |
GO:0045647 | negative regulation of erythrocyte differentiation | 0.0401401268775371 |
GO:0008301 | DNA bending activity | 0.0401401268775371 |
GO:0005721 | centric heterochromatin | 0.0401401268775371 |
GO:0016234 | inclusion body | 0.0401401268775371 |
GO:0045931 | positive regulation of progression through mitotic cell cycle | 0.0401401268775371 |
GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.0401401268775371 |
GO:0006915 | apoptosis | 0.0407460559508609 |
GO:0019955 | cytokine binding | 0.0416979237786254 |
GO:0012501 | programmed cell death | 0.0430101101597071 |
GO:0022618 | protein-RNA complex assembly | 0.0447770707926913 |
GO:0019538 | protein metabolic process | 0.0462101674809143 |
GO:0048519 | negative regulation of biological process | 0.0462101674809143 |
GO:0006929 | substrate-bound cell migration | 0.0462101674809143 |
GO:0050858 | negative regulation of antigen receptor-mediated signaling pathway | 0.0462101674809143 |
GO:0006054 | N-acetylneuraminate metabolic process | 0.0462101674809143 |
GO:0045579 | positive regulation of B cell differentiation | 0.0462101674809143 |
GO:0050860 | negative regulation of T cell receptor signaling pathway | 0.0462101674809143 |
GO:0021766 | hippocampus development | 0.0462101674809143 |
GO:0008219 | cell death | 0.0471947735251408 |
GO:0016265 | death | 0.0475058868548293 |
GO:0009059 | macromolecule biosynthetic process | 0.0478184469273156 |
GO:0035107 | appendage morphogenesis | 0.048363105703525 |
GO:0035108 | limb morphogenesis | 0.048363105703525 |
GO:0043009 | chordate embryonic development | 0.0486511061122982 |
GO:0002253 | activation of immune response | 0.0490029627721072 |
GO:0009792 | embryonic development ending in birth or egg hatching | 0.0496411960596491 |
GO:0006916 | anti-apoptosis | 0.0496411960596491 |
GO:0006366 | transcription from RNA polymerase II promoter | 0.0496713185699524 |
GO:0048736 | appendage development | 0.0498856979602618 |
GO:0060173 | limb development | 0.0498856979602618 |
GO:0048341 | paraxial mesoderm formation | 0.0498856979602618 |
GO:0045885 | positive regulation of survival gene product activity | 0.0498856979602618 |
GO:0048304 | positive regulation of isotype switching to IgG isotypes | 0.0498856979602618 |
GO:0042105 | alpha-beta T cell receptor complex | 0.0498856979602618 |
GO:0045072 | regulation of interferon-gamma biosynthetic process | 0.0498856979602618 |
GO:0006983 | ER overload response | 0.0498856979602618 |
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>
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 | 0.308688 |
MA0004.1 | 0.169566 |
MA0006.1 | 0.592722 |
MA0007.1 | 0.59656 |
MA0009.1 | 1.97209 |
MA0014.1 | 0.269368 |
MA0017.1 | 0.111761 |
MA0019.1 | 0.787164 |
MA0024.1 | 0.834595 |
MA0025.1 | 0.192731 |
MA0027.1 | 1.4282 |
MA0028.1 | 0.151944 |
MA0029.1 | 0.776087 |
MA0030.1 | 1.69175 |
MA0031.1 | 1.52823 |
MA0038.1 | 0.720173 |
MA0040.1 | 0.0823877 |
MA0041.1 | 0.143799 |
MA0042.1 | 0.00930787 |
MA0043.1 | 0.119104 |
MA0046.1 | 0.0918854 |
MA0048.1 | 0.314698 |
MA0050.1 | 0.831461 |
MA0051.1 | 0.287187 |
MA0052.1 | 0.0855944 |
MA0055.1 | 0.373954 |
MA0056.1 | 0 |
MA0057.1 | 0.494567 |
MA0058.1 | 0.0581066 |
MA0059.1 | 0.224433 |
MA0060.1 | 0.148677 |
MA0061.1 | 0.337987 |
MA0063.1 | 0 |
MA0066.1 | 0.44074 |
MA0067.1 | 0.263733 |
MA0068.1 | 0.19955 |
MA0069.1 | 0.605625 |
MA0070.1 | 0.586642 |
MA0071.1 | 0.233401 |
MA0072.1 | 0.570233 |
MA0073.1 | 0.913676 |
MA0074.1 | 0.820092 |
MA0076.1 | 0.233106 |
MA0077.1 | 0.0705161 |
MA0078.1 | 0.347428 |
MA0081.1 | 1.33768 |
MA0083.1 | 0.378154 |
MA0084.1 | 0.515655 |
MA0087.1 | 0.326314 |
MA0088.1 | 1.18081 |
MA0089.1 | 0 |
MA0090.1 | 1.24075 |
MA0091.1 | 0.00174939 |
MA0092.1 | 0.521792 |
MA0093.1 | 0.169276 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.330005 |
MA0101.1 | 0.145858 |
MA0103.1 | 0.322497 |
MA0105.1 | 0.505023 |
MA0106.1 | 0.362392 |
MA0107.1 | 0.197456 |
MA0108.2 | 0.29442 |
MA0109.1 | 0 |
MA0111.1 | 0.576007 |
MA0113.1 | 1.49601 |
MA0114.1 | 0.0128781 |
MA0115.1 | 0.382614 |
MA0116.1 | 0.591545 |
MA0117.1 | 0.105458 |
MA0119.1 | 0.7426 |
MA0122.1 | 0.367283 |
MA0124.1 | 0.228592 |
MA0125.1 | 0.183154 |
MA0130.1 | 0 |
MA0131.1 | 0.104642 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.137109 |
MA0136.1 | 0.401766 |
MA0139.1 | 0.744736 |
MA0140.1 | 0.772065 |
MA0141.1 | 0.164254 |
MA0142.1 | 0.042208 |
MA0143.1 | 0.171325 |
MA0144.1 | 0.0580936 |
MA0145.1 | 0.0274135 |
MA0146.1 | 0.349364 |
MA0147.1 | 0.873032 |
MA0148.1 | 0.729039 |
MA0149.1 | 0.00316196 |
MA0062.2 | 0.250379 |
MA0035.2 | 0.791261 |
MA0039.2 | 0.464482 |
MA0138.2 | 0.46276 |
MA0002.2 | 1.79344 |
MA0137.2 | 0.158756 |
MA0104.2 | 0.740664 |
MA0047.2 | 1.76487 |
MA0112.2 | 0.228155 |
MA0065.2 | 0.130308 |
MA0150.1 | 0.258599 |
MA0151.1 | 0 |
MA0152.1 | 0.46678 |
MA0153.1 | 0.145738 |
MA0154.1 | 0.22791 |
MA0155.1 | 0.262208 |
MA0156.1 | 0.87117 |
MA0157.1 | 0.321565 |
MA0158.1 | 0 |
MA0159.1 | 0.322927 |
MA0160.1 | 0.20053 |
MA0161.1 | 0 |
MA0162.1 | 0.722941 |
MA0163.1 | 2.08931 |
MA0164.1 | 0.402631 |
MA0080.2 | 1.24472 |
MA0018.2 | 0.243932 |
MA0099.2 | 0.0954699 |
MA0079.2 | 2.84381 |
MA0102.2 | 0.560211 |
MA0258.1 | 0.272316 |
MA0259.1 | 0.348212 |
MA0442.1 | 0 |