Coexpression cluster:C730: Difference between revisions
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Latest revision as of 11:29, 17 September 2013
Full id: C730_migratory_cord_Mast_B_b_CD14_CD19
Phase1 CAGE Peaks
Hg19::chr11:102188181..102188222,+ | p1@BIRC3 |
Hg19::chr12:97286249..97286254,+ | p@chr12:97286249..97286254 + |
Hg19::chr13:44272246..44272260,- | p@chr13:44272246..44272260 - |
Hg19::chr2:231808435..231808449,+ | p@chr2:231808435..231808449 + |
Hg19::chr2:231808494..231808516,+ | p@chr2:231808494..231808516 + |
Hg19::chr2:231808538..231808549,+ | p@chr2:231808538..231808549 + |
Hg19::chr2:231808553..231808564,+ | p@chr2:231808553..231808564 + |
Hg19::chr3:119278446..119278477,- | p1@CD80 |
Hg19::chr3:119278493..119278513,- | p3@CD80 |
Hg19::chr3:71114563..71114584,- | p49@FOXP1 |
Hg19::chr6:138192133..138192144,+ | p19@TNFAIP3 |
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
p.value | FDR | nGenes | nPathway | Name |
---|---|---|---|---|
2.51303723965872e-05 | 0.0159075257270397 | 2 | 59 | NOD-like receptor signaling pathway (KEGG):04621 |
0.000142368937182235 | 0.030165417735855 | 2 | 140 | Regulation of toll-like receptor signaling pathway (Wikipathways):WP1449 |
0.000256622577651287 | 0.0324884183306529 | 2 | 188 | TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231 |
0.000190618753465118 | 0.030165417735855 | 2 | 162 | TNF alpha/NF-kB down reg. targets (Netpath):NetPath_9 |
0.000438747620965328 | 0.0462878740118421 | 2 | 246 | B Cell Receptor up reg. targets (Netpath):NetPath_12 |
0.000174509717997661 | 0.030165417735855 | 2 | 155 | IL-1 up reg. targets (Netpath):NetPath_13 |
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 | 0.00846701689959302 |
GO:0045627 | positive regulation of T-helper 1 cell differentiation | 0.00846701689959302 |
GO:0043066 | negative regulation of apoptosis | 0.00846701689959302 |
GO:0043069 | negative regulation of programmed cell death | 0.00846701689959302 |
GO:0045425 | positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process | 0.00846701689959302 |
GO:0045625 | regulation of T-helper 1 cell differentiation | 0.00846701689959302 |
GO:0045624 | positive regulation of T-helper cell differentiation | 0.00846701689959302 |
GO:0045423 | regulation of granulocyte macrophage colony-stimulating factor biosynthetic process | 0.00846701689959302 |
GO:0045063 | T-helper 1 cell differentiation | 0.00846701689959302 |
GO:0048869 | cellular developmental process | 0.00846701689959302 |
GO:0030154 | cell differentiation | 0.00846701689959302 |
GO:0032604 | granulocyte macrophage colony-stimulating factor production | 0.00846701689959302 |
GO:0042253 | granulocyte macrophage colony-stimulating factor biosynthetic process | 0.00846701689959302 |
GO:0043124 | negative regulation of I-kappaB kinase/NF-kappaB cascade | 0.0088037535985753 |
GO:0050794 | regulation of cellular process | 0.0088037535985753 |
GO:0045622 | regulation of T-helper cell differentiation | 0.0088037535985753 |
GO:0050789 | regulation of biological process | 0.0088037535985753 |
GO:0002294 | CD4-positive, alpha-beta T cell differentiation during immune response | 0.0088037535985753 |
GO:0002292 | T cell differentiation during immune response | 0.0088037535985753 |
GO:0042093 | T-helper cell differentiation | 0.0088037535985753 |
GO:0002366 | leukocyte activation during immune response | 0.0088037535985753 |
GO:0002285 | lymphocyte activation during immune response | 0.0088037535985753 |
GO:0002293 | alpha-beta T cell differentiation during immune response | 0.0088037535985753 |
GO:0002286 | T cell activation during immune response | 0.0088037535985753 |
GO:0002263 | cell activation during immune response | 0.0088037535985753 |
GO:0043367 | CD4-positive, alpha beta T cell differentiation | 0.00896639012394077 |
GO:0045086 | positive regulation of interleukin-2 biosynthetic process | 0.00896639012394077 |
GO:0042088 | T-helper 1 type immune response | 0.00943176012279184 |
GO:0065007 | biological regulation | 0.00993040632193333 |
GO:0042981 | regulation of apoptosis | 0.0100587672340465 |
GO:0043067 | regulation of programmed cell death | 0.0100587672340465 |
GO:0045076 | regulation of interleukin-2 biosynthetic process | 0.0100587672340465 |
GO:0015026 | coreceptor activity | 0.0100587672340465 |
GO:0042094 | interleukin-2 biosynthetic process | 0.0100587672340465 |
GO:0046632 | alpha-beta T cell differentiation | 0.0100587672340465 |
GO:0050731 | positive regulation of peptidyl-tyrosine phosphorylation | 0.0103901080152437 |
GO:0046631 | alpha-beta T cell activation | 0.0112976251774761 |
GO:0032623 | interleukin-2 production | 0.0121571738180355 |
GO:0042327 | positive regulation of phosphorylation | 0.0129724438466746 |
GO:0045937 | positive regulation of phosphate metabolic process | 0.0136838464624472 |
GO:0001934 | positive regulation of protein amino acid phosphorylation | 0.0136838464624472 |
GO:0033240 | positive regulation of amine metabolic process | 0.0136838464624472 |
GO:0045764 | positive regulation of amino acid metabolic process | 0.0136838464624472 |
GO:0009966 | regulation of signal transduction | 0.0136838464624472 |
GO:0050730 | regulation of peptidyl-tyrosine phosphorylation | 0.0136838464624472 |
GO:0032502 | developmental process | 0.0143908452919003 |
GO:0006915 | apoptosis | 0.0145299318049594 |
GO:0012501 | programmed cell death | 0.0145299318049594 |
GO:0008219 | cell death | 0.0154497464175671 |
GO:0016265 | death | 0.0154497464175671 |
GO:0042108 | positive regulation of cytokine biosynthetic process | 0.0173298119070996 |
GO:0030217 | T cell differentiation | 0.0173298119070996 |
GO:0018108 | peptidyl-tyrosine phosphorylation | 0.017416768372748 |
GO:0018212 | peptidyl-tyrosine modification | 0.0177337429088587 |
GO:0001932 | regulation of protein amino acid phosphorylation | 0.0177337429088587 |
GO:0033238 | regulation of amine metabolic process | 0.0177337429088587 |
GO:0006521 | regulation of amino acid metabolic process | 0.0177337429088587 |
GO:0045727 | positive regulation of translation | 0.0200738668320086 |
GO:0048523 | negative regulation of cellular process | 0.0203475436230452 |
GO:0008270 | zinc ion binding | 0.0207769642665428 |
GO:0048519 | negative regulation of biological process | 0.0209150828709926 |
GO:0042035 | regulation of cytokine biosynthetic process | 0.0209150828709926 |
GO:0031328 | positive regulation of cellular biosynthetic process | 0.0209150828709926 |
GO:0042325 | regulation of phosphorylation | 0.0216146228805791 |
GO:0030098 | lymphocyte differentiation | 0.0216146228805791 |
GO:0048468 | cell development | 0.0216146228805791 |
GO:0042089 | cytokine biosynthetic process | 0.021638507126761 |
GO:0042107 | cytokine metabolic process | 0.021638507126761 |
GO:0051174 | regulation of phosphorus metabolic process | 0.021638507126761 |
GO:0019220 | regulation of phosphate metabolic process | 0.021638507126761 |
GO:0009891 | positive regulation of biosynthetic process | 0.0216419680822234 |
GO:0002250 | adaptive immune response | 0.0228471846603561 |
GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.0228471846603561 |
GO:0051247 | positive regulation of protein metabolic process | 0.0251974450950482 |
GO:0002521 | leukocyte differentiation | 0.0263181054783823 |
GO:0046914 | transition metal ion binding | 0.0263418696564084 |
GO:0042110 | T cell activation | 0.0279032791360802 |
GO:0009968 | negative regulation of signal transduction | 0.0290930201859787 |
GO:0007165 | signal transduction | 0.0290930201859787 |
GO:0043122 | regulation of I-kappaB kinase/NF-kappaB cascade | 0.0295843340928558 |
GO:0001816 | cytokine production | 0.030565078760423 |
GO:0018193 | peptidyl-amino acid modification | 0.0323184193172839 |
GO:0007154 | cell communication | 0.0346449739125504 |
GO:0007249 | I-kappaB kinase/NF-kappaB cascade | 0.0362133505252718 |
GO:0045595 | regulation of cell differentiation | 0.0370664343864876 |
GO:0009967 | positive regulation of signal transduction | 0.038909666557327 |
GO:0046649 | lymphocyte activation | 0.0389617623384476 |
GO:0007242 | intracellular signaling cascade | 0.039422872973318 |
GO:0030097 | hemopoiesis | 0.0395500346220457 |
GO:0004842 | ubiquitin-protein ligase activity | 0.0398340772845374 |
GO:0008639 | small protein conjugating enzyme activity | 0.0398732590749438 |
GO:0005634 | nucleus | 0.0399241594957774 |
GO:0048534 | hemopoietic or lymphoid organ development | 0.0406484365205676 |
GO:0045321 | leukocyte activation | 0.041830301086174 |
GO:0002520 | immune system development | 0.0418461718831951 |
GO:0006417 | regulation of translation | 0.0418616318815704 |
GO:0031326 | regulation of cellular biosynthetic process | 0.0447778243296604 |
GO:0043687 | post-translational protein modification | 0.0452550749111929 |
GO:0043169 | cation binding | 0.0452550749111929 |
GO:0001775 | cell activation | 0.045596969066149 |
GO:0009889 | regulation of biosynthetic process | 0.046856999686847 |
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>disease_data<br>
Ontology term | p-value | n |
---|---|---|
hemopoietic organ | 1.65e-19 | 7 |
immune organ | 1.65e-19 | 7 |
hematopoietic system | 3.62e-19 | 98 |
blood island | 3.62e-19 | 98 |
hemolymphoid system | 1.79e-18 | 108 |
immune system | 1.21e-16 | 93 |
spleen | 2.62e-12 | 3 |
gastrointestinal system mesentery | 2.62e-12 | 3 |
stomach region | 2.62e-12 | 3 |
mesentery | 2.62e-12 | 3 |
gastrointestinal system serosa | 2.62e-12 | 3 |
mesentery of stomach | 2.62e-12 | 3 |
gut mesentery | 2.62e-12 | 3 |
dorsal mesentery | 2.62e-12 | 3 |
dorsal mesogastrium | 2.62e-12 | 3 |
peritoneal cavity | 2.62e-12 | 3 |
spleen primordium | 2.62e-12 | 3 |
bone marrow | 1.48e-09 | 76 |
thymus | 2.46e-09 | 4 |
hemolymphoid system gland | 2.46e-09 | 4 |
thymic region | 2.46e-09 | 4 |
pharyngeal gland | 2.46e-09 | 4 |
thymus primordium | 2.46e-09 | 4 |
bone element | 1.30e-08 | 82 |
skeletal element | 1.49e-07 | 90 |
Ontology term | p-value | n |
---|---|---|
lymphoma | 1.45e-09 | 10 |
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 | 0.000970254 |
MA0004.1 | 0.349539 |
MA0006.1 | 0.210781 |
MA0007.1 | 0.332734 |
MA0009.1 | 0.79061 |
MA0014.1 | 0.00227771 |
MA0017.1 | 0.24363 |
MA0019.1 | 0.486183 |
MA0024.1 | 0.688373 |
MA0025.1 | 0.921763 |
MA0027.1 | 2.39404 |
MA0028.1 | 0.224112 |
MA0029.1 | 0.707146 |
MA0030.1 | 0.696006 |
MA0031.1 | 0.633489 |
MA0038.1 | 1.12886 |
MA0040.1 | 0.712837 |
MA0041.1 | 0.366339 |
MA0042.1 | 0.895841 |
MA0043.1 | 0.790919 |
MA0046.1 | 0.779945 |
MA0048.1 | 0.41425 |
MA0050.1 | 0.338274 |
MA0051.1 | 0.439895 |
MA0052.1 | 0.716602 |
MA0055.1 | 0.279754 |
MA0056.1 | 0 |
MA0057.1 | 1.08492 |
MA0058.1 | 0.265212 |
MA0059.1 | 0.2641 |
MA0060.1 | 0.119532 |
MA0061.1 | 1.12119 |
MA0063.1 | 0 |
MA0066.1 | 0.444231 |
MA0067.1 | 1.1037 |
MA0068.1 | 5.43539 |
MA0069.1 | 0.776171 |
MA0070.1 | 0.765217 |
MA0071.1 | 0.40788 |
MA0072.1 | 0.760818 |
MA0073.1 | 0.304769 |
MA0074.1 | 0.439193 |
MA0076.1 | 0.278993 |
MA0077.1 | 0.753278 |
MA0078.1 | 0.533387 |
MA0081.1 | 0.730303 |
MA0083.1 | 0.79797 |
MA0084.1 | 1.28962 |
MA0087.1 | 0.758426 |
MA0088.1 | 1.96756 |
MA0089.1 | 0 |
MA0090.1 | 0.291627 |
MA0091.1 | 0.351901 |
MA0092.1 | 1.53836 |
MA0093.1 | 0.213288 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.456802 |
MA0101.1 | 1.81378 |
MA0103.1 | 0.203171 |
MA0105.1 | 1.43099 |
MA0106.1 | 0.482519 |
MA0107.1 | 2.12117 |
MA0108.2 | 0.630531 |
MA0109.1 | 0 |
MA0111.1 | 0.303543 |
MA0113.1 | 0.498009 |
MA0114.1 | 0.153042 |
MA0115.1 | 1.02805 |
MA0116.1 | 0.159642 |
MA0117.1 | 0.827487 |
MA0119.1 | 1.99621 |
MA0122.1 | 0.852927 |
MA0124.1 | 0.98702 |
MA0125.1 | 0.904129 |
MA0130.1 | 0 |
MA0131.1 | 0.550695 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.820382 |
MA0136.1 | 0.450422 |
MA0139.1 | 0.307853 |
MA0140.1 | 0.405425 |
MA0141.1 | 0.2626 |
MA0142.1 | 0.602852 |
MA0143.1 | 0.498176 |
MA0144.1 | 0.438224 |
MA0145.1 | 0.02761 |
MA0146.1 | 0.315774 |
MA0147.1 | 0.162359 |
MA0148.1 | 0.372124 |
MA0149.1 | 0.396509 |
MA0062.2 | 0.320507 |
MA0035.2 | 0.404774 |
MA0039.2 | 0.267159 |
MA0138.2 | 3.34637 |
MA0002.2 | 0.358551 |
MA0137.2 | 0.649788 |
MA0104.2 | 0.118985 |
MA0047.2 | 0.47109 |
MA0112.2 | 0.0251803 |
MA0065.2 | 0.0286783 |
MA0150.1 | 0.781086 |
MA0151.1 | 0 |
MA0152.1 | 0.411494 |
MA0153.1 | 0.887528 |
MA0154.1 | 0.353037 |
MA0155.1 | 0.099499 |
MA0156.1 | 0.231442 |
MA0157.1 | 0.576556 |
MA0158.1 | 0 |
MA0159.1 | 0.162854 |
MA0160.1 | 0.386031 |
MA0161.1 | 0 |
MA0162.1 | 0.00470038 |
MA0163.1 | 0.232847 |
MA0164.1 | 0.509774 |
MA0080.2 | 0.21336 |
MA0018.2 | 0.483823 |
MA0099.2 | 0.411824 |
MA0079.2 | 0.0905633 |
MA0102.2 | 1.32663 |
MA0258.1 | 0.135061 |
MA0259.1 | 0.168926 |
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 |
---|---|---|---|---|
CHD2#1106 | 5 | 4.70182856096221 | 0.00236388215455891 | 0.0133963583667035 |
MEF2A#4205 | 7 | 11.9275105788644 | 3.34835558215856e-07 | 1.66444030768709e-05 |
MYC#4609 | 7 | 3.32327028193326 | 0.00150133599624924 | 0.00959068017079174 |
NFKB1#4790 | 10 | 4.98914856744894 | 3.69910541950576e-07 | 1.8223154288102e-05 |
POU2F2#5452 | 7 | 5.79480621856342 | 4.24433119609668e-05 | 0.000759550558240475 |
SPI1#6688 | 6 | 4.47508555010331 | 0.000874650134001153 | 0.00652482752463903 |
TBP#6908 | 8 | 2.69583322697919 | 0.00204085211034922 | 0.0118505812049795 |
YY1#7528 | 7 | 3.12529047717973 | 0.00219383950773288 | 0.0126440265078149 |
ZBTB33#10009 | 4 | 11.5144454654477 | 0.000274343075920951 | 0.00292517779541686 |
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.