Coexpression cluster:C8: Difference between revisions
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}} | }} |
Revision as of 17:57, 22 January 2013
Full id: C8_Natural_CD8_Basophils_CD4_CD14_Peripheral_CD34
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
p.value | FDR | nGenes | nPathway | Name |
---|---|---|---|---|
0.00024912980177805 | 0.0143362876841369 | 4 | 85 | TGF-beta signaling pathway (KEGG):04350 |
0.00123630410689459 | 0.0411884473507513 | 4 | 130 | Axon guidance (KEGG):04360 |
0.00116744088951548 | 0.0410550046146276 | 4 | 128 | Osteoclast differentiation (KEGG):04380 |
0.00149972941909355 | 0.045206129632677 | 4 | 137 | Natural killer cell mediated cytotoxicity (KEGG):04650 |
0.000619283401899587 | 0.0245003995876524 | 4 | 108 | T cell receptor signaling pathway (KEGG):04660 |
0.000962441953888537 | 0.0358368092242026 | 3 | 54 | Non-small cell lung cancer (KEGG):05223 |
1.96487710589393e-05 | 0.00248753441606171 | 6 | 154 | Integrated Breast Cancer Pathway (Wikipathways):WP1984 |
0.000527360480072809 | 0.0222546122590726 | 3 | 44 | IL-7 Signaling Pathway (Wikipathways):WP205 |
3.33914292478422e-05 | 0.00301953924484058 | 5 | 102 | IL-3 Signaling Pathway (Wikipathways):WP286 |
2.89172066216853e-05 | 0.00301953924484058 | 5 | 99 | IL-6 Signaling Pathway (Wikipathways):WP364 |
0.00157541663070587 | 0.0453290330562189 | 3 | 64 | IL-4 signaling Pathway (Wikipathways):WP395 |
0.000445806611565534 | 0.0217073527016141 | 4 | 99 | Wnt Signaling Pathway and Pluripotency (Wikipathways):WP399 |
0.00130737367667826 | 0.041378376866867 | 3 | 60 | Wnt Signaling Pathway (Wikipathways):WP363 |
1.45197942554109e-06 | 0.000459551488183754 | 5 | 54 | TGF Beta Signaling Pathway (Wikipathways):WP366 |
0.000118067655414534 | 0.00770473342746526 | 5 | 133 | T Cell Receptor Signaling Pathway (Wikipathways):WP69 |
1.30216383387807e-05 | 0.00248753441606171 | 5 | 84 | DNA damage response (only ATM dependent) (Wikipathways):WP710 |
1.9533456964218e-05 | 0.00248753441606171 | 3 | 15 | Signaling by TGF beta (Reactome):REACT_6844 |
0.000502897455470268 | 0.0222546122590726 | 8 | 511 | Signaling in Immune system (Reactome):REACT_6900 |
9.14894643775015e-07 | 0.000459551488183754 | 11 | 466 | Hemostasis (Reactome):REACT_604 |
7.44658481525793e-05 | 0.00589211023507284 | 3 | 23 | Signaling by BMP (Reactome):REACT_12034 |
0.000349621587434092 | 0.0184425387371484 | 5 | 168 | Transcription (Reactome):REACT_1788 |
0.000121717747669277 | 0.00770473342746526 | 3 | 27 | {BRCA1,28} (Static Module):NA |
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:0043231 | intracellular membrane-bound organelle | 8.63466340550882e-13 |
GO:0043227 | membrane-bound organelle | 8.63466340550882e-13 |
GO:0043229 | intracellular organelle | 9.08453071393802e-11 |
GO:0043226 | organelle | 9.08453071393802e-11 |
GO:0005634 | nucleus | 5.54501740916558e-09 |
GO:0044424 | intracellular part | 2.98202313015693e-08 |
GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 1.96337806188322e-07 |
GO:0043283 | biopolymer metabolic process | 6.60706117398259e-07 |
GO:0005622 | intracellular | 6.60706117398259e-07 |
GO:0016070 | RNA metabolic process | 6.60706117398259e-07 |
GO:0007242 | intracellular signaling cascade | 1.10931887306569e-06 |
GO:0005515 | protein binding | 2.22408867817317e-05 |
GO:0010467 | gene expression | 2.96128542105593e-05 |
GO:0044237 | cellular metabolic process | 0.000106169793040219 |
GO:0006350 | transcription | 0.000223498476167962 |
GO:0050789 | regulation of biological process | 0.00022769823470947 |
GO:0043170 | macromolecule metabolic process | 0.000415526525863495 |
GO:0065007 | biological regulation | 0.000824441906945147 |
GO:0044238 | primary metabolic process | 0.000828127332350601 |
GO:0048518 | positive regulation of biological process | 0.000828127332350601 |
GO:0044464 | cell part | 0.00084084707051449 |
GO:0050794 | regulation of cellular process | 0.0010404109317392 |
GO:0005737 | cytoplasm | 0.00125684155195159 |
GO:0048522 | positive regulation of cellular process | 0.00131627056323476 |
GO:0006351 | transcription, DNA-dependent | 0.00142407385212333 |
GO:0032774 | RNA biosynthetic process | 0.00142407385212333 |
GO:0003677 | DNA binding | 0.00200247016357857 |
GO:0006355 | regulation of transcription, DNA-dependent | 0.00349874270938066 |
GO:0044422 | organelle part | 0.00349874270938066 |
GO:0007259 | JAK-STAT cascade | 0.0040616161759669 |
GO:0045449 | regulation of transcription | 0.0040616161759669 |
GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.00539527482947222 |
GO:0016071 | mRNA metabolic process | 0.00716380069722142 |
GO:0010468 | regulation of gene expression | 0.00915107643085521 |
GO:0005625 | soluble fraction | 0.00915107643085521 |
GO:0006915 | apoptosis | 0.00915990282397495 |
GO:0012501 | programmed cell death | 0.00921262247542581 |
GO:0044446 | intracellular organelle part | 0.00921262247542581 |
GO:0007243 | protein kinase cascade | 0.0100218436677716 |
GO:0019222 | regulation of metabolic process | 0.0100392271446645 |
GO:0008219 | cell death | 0.0118416704546205 |
GO:0016265 | death | 0.0118416704546205 |
GO:0031323 | regulation of cellular metabolic process | 0.0118416704546205 |
GO:0048523 | negative regulation of cellular process | 0.0143347758769983 |
GO:0045941 | positive regulation of transcription | 0.0157700420152326 |
GO:0007165 | signal transduction | 0.0165545170260198 |
GO:0043233 | organelle lumen | 0.0166434629538912 |
GO:0031974 | membrane-enclosed lumen | 0.0166434629538912 |
GO:0045935 | positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0166434629538912 |
GO:0048519 | negative regulation of biological process | 0.0166434629538912 |
GO:0000188 | inactivation of MAPK activity | 0.0166434629538912 |
GO:0007260 | tyrosine phosphorylation of STAT protein | 0.0166434629538912 |
GO:0005739 | mitochondrion | 0.0189144079385588 |
GO:0006259 | DNA metabolic process | 0.0237005531236496 |
GO:0007049 | cell cycle | 0.0240841092722159 |
GO:0008632 | apoptotic program | 0.0254028119451839 |
GO:0043407 | negative regulation of MAP kinase activity | 0.0271146304748551 |
GO:0016049 | cell growth | 0.0284255414041407 |
GO:0008361 | regulation of cell size | 0.0305521050257172 |
GO:0031981 | nuclear lumen | 0.0309593628018811 |
GO:0004674 | protein serine/threonine kinase activity | 0.0313634835052949 |
GO:0006917 | induction of apoptosis | 0.0313634835052949 |
GO:0044428 | nuclear part | 0.0313634835052949 |
GO:0012502 | induction of programmed cell death | 0.0313634835052949 |
GO:0005654 | nucleoplasm | 0.0313634835052949 |
GO:0006396 | RNA processing | 0.031960039999801 |
GO:0042780 | tRNA 3'-end processing | 0.031960039999801 |
GO:0004810 | tRNA adenylyltransferase activity | 0.031960039999801 |
GO:0005133 | interferon-gamma receptor binding | 0.031960039999801 |
GO:0004513 | neolactotetraosylceramide alpha-2,3-sialyltransferase activity | 0.031960039999801 |
GO:0006925 | inflammatory cell apoptosis | 0.031960039999801 |
GO:0031325 | positive regulation of cellular metabolic process | 0.031998525738975 |
GO:0009617 | response to bacterium | 0.031998525738975 |
GO:0044444 | cytoplasmic part | 0.031998525738975 |
GO:0045893 | positive regulation of transcription, DNA-dependent | 0.031998525738975 |
GO:0045786 | negative regulation of progression through cell cycle | 0.0321825058191282 |
GO:0008380 | RNA splicing | 0.0321825058191282 |
GO:0004672 | protein kinase activity | 0.0346883564145511 |
GO:0006672 | ceramide metabolic process | 0.0346883564145511 |
GO:0016310 | phosphorylation | 0.0351930300932853 |
GO:0006468 | protein amino acid phosphorylation | 0.0351930300932853 |
GO:0016772 | transferase activity, transferring phosphorus-containing groups | 0.0352455966642996 |
GO:0000159 | protein phosphatase type 2A complex | 0.0368328547168756 |
GO:0009893 | positive regulation of metabolic process | 0.0368328547168756 |
GO:0007154 | cell communication | 0.0368684612560971 |
GO:0042981 | regulation of apoptosis | 0.037576799643105 |
GO:0046519 | sphingoid metabolic process | 0.0375957758701743 |
GO:0043067 | regulation of programmed cell death | 0.0386382153008559 |
GO:0044429 | mitochondrial part | 0.0412046757815468 |
GO:0042221 | response to chemical stimulus | 0.0412046757815468 |
GO:0006950 | response to stress | 0.0412046757815468 |
GO:0043065 | positive regulation of apoptosis | 0.0412046757815468 |
GO:0043068 | positive regulation of programmed cell death | 0.0412046757815468 |
GO:0004715 | non-membrane spanning protein tyrosine kinase activity | 0.0412046757815468 |
GO:0048468 | cell development | 0.0412046757815468 |
GO:0032502 | developmental process | 0.0412046757815468 |
GO:0019858 | cytosine metabolic process | 0.0412046757815468 |
GO:0016844 | strictosidine synthase activity | 0.0412046757815468 |
GO:0001574 | ganglioside biosynthetic process | 0.0412046757815468 |
GO:0016843 | amine-lyase activity | 0.0412046757815468 |
GO:0050847 | progesterone receptor signaling pathway | 0.0412046757815468 |
GO:0008148 | negative transcription elongation factor activity | 0.0412046757815468 |
GO:0032735 | positive regulation of interleukin-12 production | 0.0412046757815468 |
GO:0043270 | positive regulation of ion transport | 0.0412046757815468 |
GO:0001780 | neutrophil homeostasis | 0.0412046757815468 |
GO:0005076 | receptor signaling protein serine/threonine kinase signaling protein activity | 0.0412046757815468 |
GO:0047291 | lactosylceramide alpha-2,3-sialyltransferase activity | 0.0412046757815468 |
GO:0030617 | transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity | 0.0412046757815468 |
GO:0001781 | neutrophil apoptosis | 0.0412046757815468 |
GO:0051928 | positive regulation of calcium ion transport | 0.0412046757815468 |
GO:0018108 | peptidyl-tyrosine phosphorylation | 0.0421426256154788 |
GO:0005793 | ER-Golgi intermediate compartment | 0.0434880579257159 |
GO:0006397 | mRNA processing | 0.0434880579257159 |
GO:0022402 | cell cycle process | 0.0441357670249024 |
GO:0018212 | peptidyl-tyrosine modification | 0.044158947882047 |
GO:0007498 | mesoderm development | 0.044158947882047 |
GO:0006974 | response to DNA damage stimulus | 0.0467337113577687 |
GO:0003676 | nucleic acid binding | 0.0472507241789456 |
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><br><br>
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 |
MA0004.1 | 0.267511 |
MA0006.1 | 0.00868081 |
MA0007.1 | 0.102319 |
MA0009.1 | 3.9558 |
MA0014.1 | 0 |
MA0017.1 | 0.000848272 |
MA0019.1 | 0.364867 |
MA0024.1 | 0.374052 |
MA0025.1 | 1.26223 |
MA0027.1 | 0.369707 |
MA0028.1 | 0.00132615 |
MA0029.1 | 0.340169 |
MA0030.1 | 3.9615 |
MA0031.1 | 6.00166 |
MA0038.1 | 0.0587129 |
MA0040.1 | 0.24334 |
MA0041.1 | 1.86991 |
MA0042.1 | 3.91119 |
MA0043.1 | 0.327682 |
MA0046.1 | 0.0422268 |
MA0048.1 | 0.000158848 |
MA0050.1 | 0.537503 |
MA0051.1 | 0.0226432 |
MA0052.1 | 0.0453065 |
MA0055.1 | 0.0197093 |
MA0056.1 | 0 |
MA0057.1 | 3.56538e-07 |
MA0058.1 | 0.121643 |
MA0059.1 | 0.084143 |
MA0060.1 | 1.99654e-11 |
MA0061.1 | 27.8506 |
MA0063.1 | 0 |
MA0066.1 | 3.10064 |
MA0067.1 | 0.240848 |
MA0068.1 | 0.000687193 |
MA0069.1 | 0.600876 |
MA0070.1 | 0.17127 |
MA0071.1 | 2.4512 |
MA0072.1 | 9.085 |
MA0073.1 | 0 |
MA0074.1 | 0.368342 |
MA0076.1 | 0.0734243 |
MA0077.1 | 0.753538 |
MA0078.1 | 0.0894962 |
MA0081.1 | 0.153453 |
MA0083.1 | 0.223109 |
MA0084.1 | 0.930226 |
MA0087.1 | 0.199233 |
MA0088.1 | 1.12084e-09 |
MA0089.1 | 0 |
MA0090.1 | 0.0141579 |
MA0091.1 | 0.766852 |
MA0092.1 | 1.42812 |
MA0093.1 | 0.142197 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.0273736 |
MA0101.1 | 20.3122 |
MA0103.1 | 0.014546 |
MA0105.1 | 11.508 |
MA0106.1 | 0.205991 |
MA0107.1 | 27.883 |
MA0108.2 | 0.0179271 |
MA0109.1 | 0 |
MA0111.1 | 0.518399 |
MA0113.1 | 0.537044 |
MA0114.1 | 0.00259444 |
MA0115.1 | 0.00109324 |
MA0116.1 | 0.00282323 |
MA0117.1 | 0.424407 |
MA0119.1 | 0.592002 |
MA0122.1 | 0.370969 |
MA0124.1 | 0.368103 |
MA0125.1 | 0.0362705 |
MA0130.1 | 0 |
MA0131.1 | 0.115507 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.0276929 |
MA0136.1 | 4.06749 |
MA0139.1 | 6.11886e-08 |
MA0140.1 | 0.554737 |
MA0141.1 | 0.0770322 |
MA0142.1 | 0.309674 |
MA0143.1 | 0.30483 |
MA0144.1 | 0.525964 |
MA0145.1 | 7.95343e-06 |
MA0146.1 | 0 |
MA0147.1 | 0.008092 |
MA0148.1 | 3.17313 |
MA0149.1 | 1.77951e-11 |
MA0062.2 | 0.408863 |
MA0035.2 | 0.748514 |
MA0039.2 | 0 |
MA0138.2 | 0.00115101 |
MA0002.2 | 21.8793 |
MA0137.2 | 0.0217087 |
MA0104.2 | 2.99844e-05 |
MA0047.2 | 1.92983 |
MA0112.2 | 2.84614e-08 |
MA0065.2 | 1.14366e-05 |
MA0150.1 | 2.4938 |
MA0151.1 | 0 |
MA0152.1 | 0.0177706 |
MA0153.1 | 0.0679233 |
MA0154.1 | 0.000320227 |
MA0155.1 | 1.91432e-08 |
MA0156.1 | 7.81385 |
MA0157.1 | 3.96786 |
MA0158.1 | 0 |
MA0159.1 | 0.00223881 |
MA0160.1 | 0.96433 |
MA0161.1 | 0 |
MA0162.1 | 0 |
MA0163.1 | 0 |
MA0164.1 | 0.289357 |
MA0080.2 | 6.6003 |
MA0018.2 | 2.26782 |
MA0099.2 | 2.29962 |
MA0079.2 | 0 |
MA0102.2 | 0.30425 |
MA0258.1 | 0.156209 |
MA0259.1 | 0.000218999 |
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 |
---|---|---|---|---|
BATF#10538 | 208 | 3.34638228058068 | 7.96257119070932e-52 | 6.11472773960655e-49 |
BCL11A#53335 | 227 | 4.25354445741004 | 3.26153564180878e-75 | 3.87081273744167e-72 |
BCL3#602 | 124 | 2.82948530228768 | 2.07423544351374e-24 | 6.44735343705749e-22 |
CEBPB#1051 | 241 | 1.26885507121782 | 6.80057249868787e-05 | 0.00108649991003589 |
EBF1#1879 | 452 | 2.65899802816987 | 1.59379437648377e-86 | 2.1070163403239e-83 |
ELF1#1997 | 438 | 1.23186717698659 | 5.42659154992983e-07 | 2.51440902787543e-05 |
EP300#2033 | 304 | 1.36015738756397 | 1.19405252342936e-08 | 8.91391361647169e-07 |
FOS#2353 | 238 | 1.41447382002435 | 3.21996077710046e-08 | 2.16960957161029e-06 |
FOSL1#8061 | 68 | 1.78370107048439 | 5.42555123003451e-06 | 0.000165587125924481 |
FOXA1#3169 | 168 | 1.22964234999786 | 0.00339576263211426 | 0.0173278962982059 |
FOXA2#3170 | 80 | 1.30147760912366 | 0.0113429073116636 | 0.0415941117489848 |
GATA1#2623 | 162 | 1.45097088460744 | 1.64261712851743e-06 | 6.22472025708388e-05 |
GATA2#2624 | 198 | 1.66677442750574 | 1.612389522416e-12 | 2.21866072900665e-10 |
IRF4#3662 | 174 | 2.51857675527971 | 2.9589891052122e-28 | 1.08432934441845e-25 |
JUN#3725 | 205 | 1.69427343753563 | 1.33492803586132e-13 | 2.05935818518937e-11 |
JUNB#3726 | 76 | 1.53659714804915 | 0.000201730544070915 | 0.0023966029225597 |
JUND#3727 | 255 | 1.17809729536137 | 0.00297612484105929 | 0.0158623884804997 |
MAX#4149 | 269 | 1.14645801315913 | 0.00869184742202502 | 0.0330253520904017 |
MEF2A#4205 | 188 | 2.32742893726095 | 1.76653948863028e-26 | 6.00962923951328e-24 |
MEF2C#4208 | 83 | 2.26475721458903 | 1.33582051403411e-11 | 1.65102672976579e-09 |
MXI1#4601 | 183 | 1.20407371734673 | 0.00523176558163341 | 0.0242413649325737 |
NFKB1#4790 | 556 | 2.01543148206854 | 2.54187348868515e-65 | 2.55260312773835e-62 |
NR4A1#3164 | 4 | 7.28827461109249 | 0.00228227912794635 | 0.0129549948281748 |
PAX5#5079 | 401 | 1.76650976089981 | 3.10127007246155e-31 | 1.31130989918143e-28 |
PBX3#5090 | 114 | 1.65010201207981 | 2.03474580505133e-07 | 1.09879429748581e-05 |
POLR2A#5430 | 861 | 1.22123988442305 | 4.70592212466373e-16 | 9.1353494568356e-14 |
POU2F2#5452 | 311 | 1.87054463801712 | 1.59517504349045e-27 | 5.74477539196892e-25 |
RFX5#5993 | 162 | 1.28914237384782 | 0.000606796035273713 | 0.00506661105915825 |
SMARCB1#6598 | 105 | 1.26587526883853 | 0.008877361268895 | 0.0336824360082149 |
SMARCC1#6599 | 63 | 1.81690332703883 | 6.81763355733294e-06 | 0.000198225732487276 |
SP1#6667 | 336 | 1.26463417639058 | 2.13024321125317e-06 | 7.75193277839963e-05 |
SPI1#6688 | 322 | 1.74490896284301 | 1.40948911000144e-23 | 4.26682994665046e-21 |
STAT3#6774 | 176 | 1.22287043560049 | 0.00339552128690622 | 0.0173275113692563 |
TAL1#6886 | 90 | 1.77554524502617 | 2.06052981289665e-07 | 1.10585649089986e-05 |
TCF12#6938 | 253 | 1.77709354045784 | 2.87714246728154e-19 | 6.89187803074351e-17 |
WRNIP1#56897 | 24 | 1.7408712974802 | 0.00735156150730021 | 0.0303954763365371 |
ZEB1#6935 | 139 | 1.55052315088415 | 3.08364634856496e-07 | 1.5490761952755e-05 |
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