Coexpression cluster:C817: Difference between revisions
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Latest revision as of 11:31, 17 September 2013
Full id: C817_cord_CD14_mycosis_xeroderma_migratory_B_hairy
Phase1 CAGE Peaks
Hg19::chr12:24858680..24858711,- | p@chr12:24858680..24858711 - |
Hg19::chr12:39300630..39300641,- | p@chr12:39300630..39300641 - |
Hg19::chr12:47787958..47787968,- | p@chr12:47787958..47787968 - |
Hg19::chr17:40440359..40440386,+ | p4@STAT5A |
Hg19::chr2:223288634..223288698,+ | p2@SGPP2 |
Hg19::chr3:47032286..47032317,+ | p@chr3:47032286..47032317 + |
Hg19::chr6:138192164..138192180,+ | p4@TNFAIP3 |
Hg19::chr6:138192205..138192214,+ | p15@TNFAIP3 |
Hg19::chr6:138192259..138192268,+ | p18@TNFAIP3 |
Hg19::chr8:145086442..145086455,+ | p2@SPATC1 |
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
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
GO ID | GO name | FDR corrected p-value |
---|---|---|
GO:0006916 | anti-apoptosis | 0.0098087440622032 |
GO:0046544 | development of secondary male sexual characteristics | 0.0098087440622032 |
GO:0001779 | natural killer cell differentiation | 0.0098087440622032 |
GO:0001553 | luteinization | 0.0098087440622032 |
GO:0046543 | development of secondary female sexual characteristics | 0.0098087440622032 |
GO:0043066 | negative regulation of apoptosis | 0.0098087440622032 |
GO:0043069 | negative regulation of programmed cell death | 0.0098087440622032 |
GO:0045136 | development of secondary sexual characteristics | 0.010829102476073 |
GO:0045647 | negative regulation of erythrocyte differentiation | 0.010829102476073 |
GO:0045579 | positive regulation of B cell differentiation | 0.010829102476073 |
GO:0045931 | positive regulation of progression through mitotic cell cycle | 0.010829102476073 |
GO:0043029 | T cell homeostasis | 0.010829102476073 |
GO:0042104 | positive regulation of activated T cell proliferation | 0.010829102476073 |
GO:0043124 | negative regulation of I-kappaB kinase/NF-kappaB cascade | 0.010829102476073 |
GO:0007243 | protein kinase cascade | 0.010829102476073 |
GO:0045621 | positive regulation of lymphocyte differentiation | 0.010829102476073 |
GO:0046006 | regulation of activated T cell proliferation | 0.010829102476073 |
GO:0030856 | regulation of epithelial cell differentiation | 0.010829102476073 |
GO:0050798 | activated T cell proliferation | 0.010829102476073 |
GO:0019915 | sequestering of lipid | 0.010829102476073 |
GO:0045885 | positive regulation of survival gene product activity | 0.010829102476073 |
GO:0045577 | regulation of B cell differentiation | 0.010829102476073 |
GO:0019218 | regulation of steroid metabolic process | 0.0116977484600152 |
GO:0002260 | lymphocyte homeostasis | 0.0116977484600152 |
GO:0050729 | positive regulation of inflammatory response | 0.0116977484600152 |
GO:0045086 | positive regulation of interleukin-2 biosynthetic process | 0.0116977484600152 |
GO:0031349 | positive regulation of defense response | 0.0116977484600152 |
GO:0045646 | regulation of erythrocyte differentiation | 0.0116977484600152 |
GO:0040018 | positive regulation of multicellular organism growth | 0.0123205953733832 |
GO:0030879 | mammary gland development | 0.0125345319247793 |
GO:0001776 | leukocyte homeostasis | 0.0125345319247793 |
GO:0042981 | regulation of apoptosis | 0.0125345319247793 |
GO:0043067 | regulation of programmed cell death | 0.0125345319247793 |
GO:0048872 | homeostasis of number of cells | 0.0125345319247793 |
GO:0045076 | regulation of interleukin-2 biosynthetic process | 0.0125345319247793 |
GO:0045884 | regulation of survival gene product activity | 0.0125345319247793 |
GO:0042094 | interleukin-2 biosynthetic process | 0.0125345319247793 |
GO:0045619 | regulation of lymphocyte differentiation | 0.0125345319247793 |
GO:0030101 | natural killer cell activation | 0.0130683881921848 |
GO:0050871 | positive regulation of B cell activation | 0.0130683881921848 |
GO:0045638 | negative regulation of myeloid cell differentiation | 0.0130683881921848 |
GO:0005737 | cytoplasm | 0.0137767055420435 |
GO:0032623 | interleukin-2 production | 0.0137767055420435 |
GO:0007595 | lactation | 0.0137767055420435 |
GO:0040014 | regulation of multicellular organism growth | 0.0137767055420435 |
GO:0045927 | positive regulation of growth | 0.0137767055420435 |
GO:0035264 | multicellular organism growth | 0.0137767055420435 |
GO:0045787 | positive regulation of progression through cell cycle | 0.0137767055420435 |
GO:0022601 | menstrual cycle phase | 0.0137767055420435 |
GO:0031347 | regulation of defense response | 0.0137767055420435 |
GO:0050727 | regulation of inflammatory response | 0.0137767055420435 |
GO:0042102 | positive regulation of T cell proliferation | 0.0137767055420435 |
GO:0022602 | menstrual cycle process | 0.0137767055420435 |
GO:0050864 | regulation of B cell activation | 0.0137767055420435 |
GO:0008585 | female gonad development | 0.0145156931210802 |
GO:0019216 | regulation of lipid metabolic process | 0.0145156931210802 |
GO:0030183 | B cell differentiation | 0.0145156931210802 |
GO:0046545 | development of primary female sexual characteristics | 0.0145156931210802 |
GO:0046660 | female sex differentiation | 0.0145156931210802 |
GO:0032946 | positive regulation of mononuclear cell proliferation | 0.0145156931210802 |
GO:0050671 | positive regulation of lymphocyte proliferation | 0.0145156931210802 |
GO:0006915 | apoptosis | 0.0145156931210802 |
GO:0012501 | programmed cell death | 0.0145156931210802 |
GO:0046661 | male sex differentiation | 0.0145156931210802 |
GO:0007346 | regulation of progression through mitotic cell cycle | 0.0145156931210802 |
GO:0030218 | erythrocyte differentiation | 0.0145156931210802 |
GO:0042698 | menstrual cycle | 0.0145156931210802 |
GO:0042129 | regulation of T cell proliferation | 0.0145156931210802 |
GO:0045637 | regulation of myeloid cell differentiation | 0.0145156931210802 |
GO:0048583 | regulation of response to stimulus | 0.0145156931210802 |
GO:0008219 | cell death | 0.0145156931210802 |
GO:0016265 | death | 0.0145156931210802 |
GO:0030855 | epithelial cell differentiation | 0.0146678950118608 |
GO:0042098 | T cell proliferation | 0.0154644313545556 |
GO:0007259 | JAK-STAT cascade | 0.0154644313545556 |
GO:0042108 | positive regulation of cytokine biosynthetic process | 0.0158086676443632 |
GO:0050870 | positive regulation of T cell activation | 0.0158086676443632 |
GO:0050670 | regulation of lymphocyte proliferation | 0.0158086676443632 |
GO:0032944 | regulation of mononuclear cell proliferation | 0.0158086676443632 |
GO:0019221 | cytokine and chemokine mediated signaling pathway | 0.0159820453218798 |
GO:0048732 | gland development | 0.0168837595886084 |
GO:0051251 | positive regulation of lymphocyte activation | 0.0181058406720078 |
GO:0008406 | gonad development | 0.0181058406720078 |
GO:0048608 | reproductive structure development | 0.0181058406720078 |
GO:0032943 | mononuclear cell proliferation | 0.0181058406720078 |
GO:0045727 | positive regulation of translation | 0.0181058406720078 |
GO:0046651 | lymphocyte proliferation | 0.0181058406720078 |
GO:0048523 | negative regulation of cellular process | 0.0184569630324013 |
GO:0048519 | negative regulation of biological process | 0.0188784886440321 |
GO:0050863 | regulation of T cell activation | 0.0188784886440321 |
GO:0045137 | development of primary sexual characteristics | 0.0188784886440321 |
GO:0042035 | regulation of cytokine biosynthetic process | 0.0188784886440321 |
GO:0031328 | positive regulation of cellular biosynthetic process | 0.0188784886440321 |
GO:0048609 | reproductive process in a multicellular organism | 0.0188784886440321 |
GO:0032504 | multicellular organism reproduction | 0.0188784886440321 |
GO:0042113 | B cell activation | 0.0188784886440321 |
GO:0002009 | morphogenesis of an epithelium | 0.0192947462408728 |
GO:0030098 | lymphocyte differentiation | 0.0193083537645488 |
GO:0048468 | cell development | 0.0193083537645488 |
GO:0045596 | negative regulation of cell differentiation | 0.0193083537645488 |
GO:0030155 | regulation of cell adhesion | 0.019410435056621 |
GO:0042089 | cytokine biosynthetic process | 0.0195104890621031 |
GO:0042107 | cytokine metabolic process | 0.0196085748296782 |
GO:0009891 | positive regulation of biosynthetic process | 0.019989442238841 |
GO:0051249 | regulation of lymphocyte activation | 0.0213652824192219 |
GO:0030099 | myeloid cell differentiation | 0.0213652824192219 |
GO:0051093 | negative regulation of developmental process | 0.0213652824192219 |
GO:0050865 | regulation of cell activation | 0.0218583455770107 |
GO:0007565 | female pregnancy | 0.0218583455770107 |
GO:0007548 | sex differentiation | 0.0218583455770107 |
GO:0051247 | positive regulation of protein metabolic process | 0.0225908458224773 |
GO:0043229 | intracellular organelle | 0.0225908458224773 |
GO:0043226 | organelle | 0.0225908458224773 |
GO:0003006 | reproductive developmental process | 0.022647707531505 |
GO:0002521 | leukocyte differentiation | 0.0232218577750432 |
GO:0042110 | T cell activation | 0.0250591822261653 |
GO:0009968 | negative regulation of signal transduction | 0.0263591358542017 |
GO:0043122 | regulation of I-kappaB kinase/NF-kappaB cascade | 0.0271361788289405 |
GO:0001816 | cytokine production | 0.028147672630088 |
GO:0005813 | centrosome | 0.0318428891726392 |
GO:0048869 | cellular developmental process | 0.0328468075171884 |
GO:0030154 | cell differentiation | 0.0328468075171884 |
GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 0.0331898449785698 |
GO:0007249 | I-kappaB kinase/NF-kappaB cascade | 0.0331898449785698 |
GO:0045595 | regulation of cell differentiation | 0.0341011196355686 |
GO:0005815 | microtubule organizing center | 0.0345306996525982 |
GO:0046649 | lymphocyte activation | 0.0361104615281305 |
GO:0007242 | intracellular signaling cascade | 0.0366690693465053 |
GO:0030097 | hemopoiesis | 0.0369169725815447 |
GO:0048534 | hemopoietic or lymphoid organ development | 0.0393425365237529 |
GO:0045321 | leukocyte activation | 0.0404395778703146 |
GO:0044424 | intracellular part | 0.0404395778703146 |
GO:0002520 | immune system development | 0.0404395778703146 |
GO:0006417 | regulation of translation | 0.0405752779607144 |
GO:0031326 | regulation of cellular biosynthetic process | 0.0435291181174172 |
GO:0040008 | regulation of growth | 0.0436394550898104 |
GO:0001775 | cell activation | 0.0450292094685027 |
GO:0009889 | regulation of biosynthetic process | 0.0463976173369759 |
GO:0045893 | positive regulation of transcription, DNA-dependent | 0.0469868872906378 |
GO:0008202 | steroid metabolic process | 0.0469868872906378 |
GO:0008284 | positive regulation of cell proliferation | 0.0487241955275788 |
GO:0050793 | regulation of developmental process | 0.0489975011728461 |
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>
Ontology term | p-value | n |
---|---|---|
hematopoietic system | 3.44e-41 | 98 |
blood island | 3.44e-41 | 98 |
hemolymphoid system | 2.02e-39 | 108 |
immune system | 1.00e-37 | 93 |
bone marrow | 1.27e-34 | 76 |
bone element | 3.63e-31 | 82 |
skeletal element | 2.78e-27 | 90 |
skeletal system | 2.59e-23 | 100 |
lateral plate mesoderm | 3.93e-15 | 203 |
musculoskeletal system | 5.25e-10 | 167 |
connective tissue | 5.94e-10 | 371 |
mesoderm | 8.42e-09 | 315 |
mesoderm-derived structure | 8.42e-09 | 315 |
presumptive mesoderm | 8.42e-09 | 315 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<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 | 0.0250581 |
MA0004.1 | 0.380329 |
MA0006.1 | 0.236135 |
MA0007.1 | 1.69684 |
MA0009.1 | 0.828613 |
MA0014.1 | 0.15363 |
MA0017.1 | 0.270554 |
MA0019.1 | 0.520264 |
MA0024.1 | 0.725404 |
MA0025.1 | 2.20595 |
MA0027.1 | 2.43535 |
MA0028.1 | 0.25013 |
MA0029.1 | 2.9484 |
MA0030.1 | 0.733118 |
MA0031.1 | 0.669876 |
MA0038.1 | 0.477043 |
MA0040.1 | 0.750125 |
MA0041.1 | 0.397617 |
MA0042.1 | 0.367902 |
MA0043.1 | 0.828925 |
MA0046.1 | 0.817858 |
MA0048.1 | 0.220931 |
MA0050.1 | 0.368721 |
MA0051.1 | 0.473017 |
MA0052.1 | 0.753928 |
MA0055.1 | 0.174262 |
MA0056.1 | 0 |
MA0057.1 | 0.211138 |
MA0058.1 | 0.293055 |
MA0059.1 | 0.291897 |
MA0060.1 | 0.138988 |
MA0061.1 | 3.1466 |
MA0063.1 | 0 |
MA0066.1 | 0.477449 |
MA0067.1 | 1.1435 |
MA0068.1 | 0.631708 |
MA0069.1 | 0.814052 |
MA0070.1 | 0.803003 |
MA0071.1 | 0.440254 |
MA0072.1 | 0.798564 |
MA0073.1 | 0.00880943 |
MA0074.1 | 0.4723 |
MA0076.1 | 0.307383 |
MA0077.1 | 0.790956 |
MA0078.1 | 0.568317 |
MA0081.1 | 0.79376 |
MA0083.1 | 0.836033 |
MA0084.1 | 1.32998 |
MA0087.1 | 0.79615 |
MA0088.1 | 0.55119 |
MA0089.1 | 0 |
MA0090.1 | 1.54714 |
MA0091.1 | 0.382762 |
MA0092.1 | 0.347826 |
MA0093.1 | 0.238771 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.49029 |
MA0101.1 | 6.5191 |
MA0103.1 | 0.646502 |
MA0105.1 | 2.12449 |
MA0106.1 | 0.516528 |
MA0107.1 | 5.66423 |
MA0108.2 | 0.666881 |
MA0109.1 | 0 |
MA0111.1 | 0.885497 |
MA0113.1 | 0.532314 |
MA0114.1 | 0.174997 |
MA0115.1 | 1.06753 |
MA0116.1 | 0.182037 |
MA0117.1 | 0.865782 |
MA0119.1 | 3.88311 |
MA0122.1 | 0.891407 |
MA0124.1 | 1.0263 |
MA0125.1 | 0.942948 |
MA0130.1 | 0 |
MA0131.1 | 0.585907 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.858623 |
MA0136.1 | 0.483775 |
MA0139.1 | 0.353333 |
MA0140.1 | 0.437738 |
MA0141.1 | 0.290336 |
MA0142.1 | 1.54256 |
MA0143.1 | 0.532484 |
MA0144.1 | 1.51733 |
MA0145.1 | 0.0359093 |
MA0146.1 | 0.128432 |
MA0147.1 | 0.184931 |
MA0148.1 | 0.403564 |
MA0149.1 | 0.428597 |
MA0062.2 | 0.114378 |
MA0035.2 | 0.437071 |
MA0039.2 | 0.0109452 |
MA0138.2 | 0.569505 |
MA0002.2 | 0.129981 |
MA0137.2 | 2.02481 |
MA0104.2 | 0.138396 |
MA0047.2 | 0.504873 |
MA0112.2 | 0.133417 |
MA0065.2 | 0.615279 |
MA0150.1 | 0.315136 |
MA0151.1 | 0 |
MA0152.1 | 0.443956 |
MA0153.1 | 0.926242 |
MA0154.1 | 1.12157 |
MA0155.1 | 0.030416 |
MA0156.1 | 0.257809 |
MA0157.1 | 1.4867 |
MA0158.1 | 0 |
MA0159.1 | 0.185458 |
MA0160.1 | 0.417847 |
MA0161.1 | 0 |
MA0162.1 | 0.108522 |
MA0163.1 | 0.0728181 |
MA0164.1 | 0.544294 |
MA0080.2 | 0.671553 |
MA0018.2 | 0.517858 |
MA0099.2 | 0.444294 |
MA0079.2 | 0.0179307 |
MA0102.2 | 1.36707 |
MA0258.1 | 0.472117 |
MA0259.1 | 0.560522 |
MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
TF | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
EBF1#1879 | 6 | 5.3438801079414 | 0.000280926593131646 | 0.00298988000204585 |
IRF4#3662 | 5 | 10.9572563433721 | 4.10495409675721e-05 | 0.000745854733666017 |
NFKB1#4790 | 9 | 4.93925708177445 | 1.84959706943667e-06 | 6.85973254030173e-05 |
TCF12#6938 | 4 | 4.25378596087457 | 0.0103111806051884 | 0.0383002948829986 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.