Coexpression cluster:C1768: Difference between revisions
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{{Coexpression_clusters | 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formyltransferase activity!0.0027375485694101!2618$GO:0004641!phosphoribosylformylglycinamidine cyclo-ligase activity!0.0027375485694101!2618$GO:0004637!phosphoribosylamine-glycine ligase activity!0.00456231233278836!2618$GO:0046040!IMP metabolic process!0.00456231233278836!2618$GO:0006189!'de novo' IMP biosynthetic process!0.00456231233278836!2618$GO:0006188!IMP biosynthetic process!0.00456231233278836!2618$GO:0009113!purine base biosynthetic process!0.00547461362960894!2618$GO:0016882!cyclo-ligase activity!0.00602172041914822!2618$GO:0006144!purine base metabolic process!0.00602172041914822!2618$GO:0016742!hydroxymethyl-, formyl- and related transferase activity!0.00602172041914822!2618$GO:0046112!nucleobase biosynthetic process!0.00696697213612794!2618$GO:0009112!nucleobase metabolic process!0.00855181734683608!2618$GO:0009168!purine ribonucleoside monophosphate biosynthetic process!0.00855181734683608!2618$GO:0009167!purine ribonucleoside monophosphate metabolic process!0.00855181734683608!2618$GO:0009127!purine nucleoside monophosphate biosynthetic process!0.00855181734683608!2618$GO:0009126!purine nucleoside monophosphate metabolic process!0.00855181734683608!2618$GO:0004372!glycine hydroxymethyltransferase activity!0.00901422339566733!2618$GO:0009161!ribonucleoside monophosphate metabolic process!0.00945183586136322!2618$GO:0009156!ribonucleoside monophosphate biosynthetic process!0.00945183586136322!2618$GO:0046148!pigment biosynthetic process!0.00945183586136322!2618$GO:0009124!nucleoside monophosphate biosynthetic process!0.00945183586136322!2618$GO:0009123!nucleoside monophosphate metabolic process!0.00945183586136322!2618$GO:0042440!pigment metabolic process!0.00999197011681788!2618$GO:0019748!secondary metabolic process!0.0120815856858232!2618$GO:0005524!ATP binding!0.0245517609060341!204851;2618$GO:0032559!adenyl ribonucleotide binding!0.0245517609060341!204851;2618$GO:0030554!adenyl nucleotide binding!0.0253718292786105!204851;2618$GO:0046483!heterocycle metabolic process!0.0253718292786105!2618$GO:0009152!purine ribonucleotide biosynthetic process!0.0262962846519019!2618$GO:0009150!purine ribonucleotide metabolic process!0.0262962846519019!2618$GO:0009260!ribonucleotide biosynthetic process!0.0262962846519019!2618$GO:0016740!transferase activity!0.0262962846519019!204851;2618$GO:0006164!purine nucleotide biosynthetic process!0.0262962846519019!2618$GO:0006163!purine nucleotide metabolic process!0.0262962846519019!2618$GO:0009259!ribonucleotide metabolic process!0.0262962846519019!2618$GO:0032553!ribonucleotide binding!0.0262962846519019!204851;2618$GO:0032555!purine ribonucleotide binding!0.0262962846519019!204851;2618$GO:0006725!aromatic compound metabolic process!0.0262962846519019!2618$GO:0017076!purine nucleotide binding!0.0273848872620982!204851;2618$GO:0009165!nucleotide biosynthetic process!0.0347732572115841!2618$GO:0000166!nucleotide 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| ||
|full_id=C1768_testis_CD8_Natural_embryonic_Eosinophils_CD4_CD14 | |||
|id=C1768 | |||
}} | |||
Latest revision as of 11:51, 17 September 2013
Full id: C1768_testis_CD8_Natural_embryonic_Eosinophils_CD4_CD14
Phase1 CAGE Peaks
| Hg19::chr16:85833874..85833901,+ | p@chr16:85833874..85833901 + |
| Hg19::chr1:114471972..114472000,+ | p3@HIPK1 |
| Hg19::chr21:34915147..34915178,- | p3@GART |
| Hg19::chr21:34915181..34915204,- | p4@GART |
| Hg19::chr5:34839260..34839339,+ | p1@TTC23L |
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:0004644 | phosphoribosylglycinamide formyltransferase activity | 0.0027375485694101 |
| GO:0004641 | phosphoribosylformylglycinamidine cyclo-ligase activity | 0.0027375485694101 |
| GO:0004637 | phosphoribosylamine-glycine ligase activity | 0.00456231233278836 |
| GO:0046040 | IMP metabolic process | 0.00456231233278836 |
| GO:0006189 | 'de novo' IMP biosynthetic process | 0.00456231233278836 |
| GO:0006188 | IMP biosynthetic process | 0.00456231233278836 |
| GO:0009113 | purine base biosynthetic process | 0.00547461362960894 |
| GO:0016882 | cyclo-ligase activity | 0.00602172041914822 |
| GO:0006144 | purine base metabolic process | 0.00602172041914822 |
| GO:0016742 | hydroxymethyl-, formyl- and related transferase activity | 0.00602172041914822 |
| GO:0046112 | nucleobase biosynthetic process | 0.00696697213612794 |
| GO:0009112 | nucleobase metabolic process | 0.00855181734683608 |
| GO:0009168 | purine ribonucleoside monophosphate biosynthetic process | 0.00855181734683608 |
| GO:0009167 | purine ribonucleoside monophosphate metabolic process | 0.00855181734683608 |
| GO:0009127 | purine nucleoside monophosphate biosynthetic process | 0.00855181734683608 |
| GO:0009126 | purine nucleoside monophosphate metabolic process | 0.00855181734683608 |
| GO:0004372 | glycine hydroxymethyltransferase activity | 0.00901422339566733 |
| GO:0009161 | ribonucleoside monophosphate metabolic process | 0.00945183586136322 |
| GO:0009156 | ribonucleoside monophosphate biosynthetic process | 0.00945183586136322 |
| GO:0046148 | pigment biosynthetic process | 0.00945183586136322 |
| GO:0009124 | nucleoside monophosphate biosynthetic process | 0.00945183586136322 |
| GO:0009123 | nucleoside monophosphate metabolic process | 0.00945183586136322 |
| GO:0042440 | pigment metabolic process | 0.00999197011681788 |
| GO:0019748 | secondary metabolic process | 0.0120815856858232 |
| GO:0005524 | ATP binding | 0.0245517609060341 |
| GO:0032559 | adenyl ribonucleotide binding | 0.0245517609060341 |
| GO:0030554 | adenyl nucleotide binding | 0.0253718292786105 |
| GO:0046483 | heterocycle metabolic process | 0.0253718292786105 |
| GO:0009152 | purine ribonucleotide biosynthetic process | 0.0262962846519019 |
| GO:0009150 | purine ribonucleotide metabolic process | 0.0262962846519019 |
| GO:0009260 | ribonucleotide biosynthetic process | 0.0262962846519019 |
| GO:0016740 | transferase activity | 0.0262962846519019 |
| GO:0006164 | purine nucleotide biosynthetic process | 0.0262962846519019 |
| GO:0006163 | purine nucleotide metabolic process | 0.0262962846519019 |
| GO:0009259 | ribonucleotide metabolic process | 0.0262962846519019 |
| GO:0032553 | ribonucleotide binding | 0.0262962846519019 |
| GO:0032555 | purine ribonucleotide binding | 0.0262962846519019 |
| GO:0006725 | aromatic compound metabolic process | 0.0262962846519019 |
| GO:0017076 | purine nucleotide binding | 0.0273848872620982 |
| GO:0009165 | nucleotide biosynthetic process | 0.0347732572115841 |
| GO:0000166 | nucleotide binding | 0.0351870221378261 |
| GO:0008168 | methyltransferase activity | 0.0351870221378261 |
| GO:0016741 | transferase activity, transferring one-carbon groups | 0.0352528252605742 |
| GO:0009117 | nucleotide metabolic process | 0.042096473073867 |
| GO:0055086 | nucleobase, nucleoside and nucleotide metabolic process | 0.0439173729042794 |
| GO:0016879 | ligase activity, forming carbon-nitrogen bonds | 0.0439173729042794 |
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 |
|---|---|---|
| classical monocyte | 2.64e-35 | 42 |
| CD14-positive, CD16-negative classical monocyte | 2.64e-35 | 42 |
| leukocyte | 2.73e-31 | 136 |
| defensive cell | 1.54e-28 | 48 |
| phagocyte | 1.54e-28 | 48 |
| myeloid leukocyte | 4.87e-28 | 72 |
| hematopoietic lineage restricted progenitor cell | 6.37e-27 | 120 |
| nongranular leukocyte | 4.78e-24 | 115 |
| myeloid lineage restricted progenitor cell | 7.23e-24 | 66 |
| granulocyte monocyte progenitor cell | 9.83e-24 | 67 |
| macrophage dendritic cell progenitor | 1.94e-22 | 61 |
| hematopoietic stem cell | 3.70e-22 | 168 |
| angioblastic mesenchymal cell | 3.70e-22 | 168 |
| monopoietic cell | 5.31e-21 | 59 |
| monocyte | 5.31e-21 | 59 |
| monoblast | 5.31e-21 | 59 |
| promonocyte | 5.31e-21 | 59 |
| hematopoietic cell | 7.31e-21 | 177 |
| hematopoietic oligopotent progenitor cell | 1.59e-19 | 161 |
| hematopoietic multipotent progenitor cell | 1.59e-19 | 161 |
| myeloid cell | 1.66e-15 | 108 |
| common myeloid progenitor | 1.66e-15 | 108 |
| stuff accumulating cell | 1.15e-12 | 87 |
| intermediate monocyte | 1.90e-08 | 9 |
| CD14-positive, CD16-positive monocyte | 1.90e-08 | 9 |
| Ontology term | p-value | n |
|---|---|---|
| bone marrow | 7.33e-21 | 76 |
| hematopoietic system | 4.42e-20 | 98 |
| blood island | 4.42e-20 | 98 |
| bone element | 1.09e-19 | 82 |
| skeletal element | 1.38e-17 | 90 |
| immune system | 1.31e-16 | 93 |
| hemolymphoid system | 3.30e-16 | 108 |
| skeletal system | 1.26e-14 | 100 |
| neural tube | 8.88e-12 | 56 |
| neural rod | 8.88e-12 | 56 |
| future spinal cord | 8.88e-12 | 56 |
| neural keel | 8.88e-12 | 56 |
| regional part of nervous system | 3.40e-11 | 53 |
| regional part of brain | 3.40e-11 | 53 |
| regional part of forebrain | 1.73e-09 | 41 |
| forebrain | 1.73e-09 | 41 |
| anterior neural tube | 1.73e-09 | 41 |
| future forebrain | 1.73e-09 | 41 |
| brain grey matter | 1.30e-08 | 34 |
| gray matter | 1.30e-08 | 34 |
| central nervous system | 1.72e-08 | 81 |
| neocortex | 1.73e-08 | 20 |
| brain | 2.83e-08 | 68 |
| future brain | 2.83e-08 | 68 |
| telencephalon | 3.72e-08 | 34 |
| regional part of telencephalon | 1.41e-07 | 32 |
| cerebral hemisphere | 1.76e-07 | 32 |
| nervous system | 2.49e-07 | 89 |
| regional part of cerebral cortex | 2.75e-07 | 22 |
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 | 0.481059 |
| MA0004.1 | 0.626788 |
| MA0006.1 | 0.452993 |
| MA0007.1 | 0.606704 |
| MA0009.1 | 1.11255 |
| MA0014.1 | 0.161847 |
| MA0017.1 | 1.24112 |
| MA0019.1 | 0.784036 |
| MA0024.1 | 1.00439 |
| MA0025.1 | 1.24931 |
| MA0027.1 | 2.73598 |
| MA0028.1 | 0.470679 |
| MA0029.1 | 1.02437 |
| MA0030.1 | 1.01252 |
| MA0031.1 | 0.945567 |
| MA0038.1 | 1.7452 |
| MA0040.1 | 1.03042 |
| MA0041.1 | 0.64667 |
| MA0042.1 | 0.612397 |
| MA0043.1 | 1.11288 |
| MA0046.1 | 1.10134 |
| MA0048.1 | 0.569896 |
| MA0050.1 | 0.613347 |
| MA0051.1 | 0.731787 |
| MA0052.1 | 1.03442 |
| MA0055.1 | 0.0853006 |
| MA0056.1 | 0 |
| MA0057.1 | 0.189508 |
| MA0058.1 | 0.523638 |
| MA0059.1 | 0.522232 |
| MA0060.1 | 2.35759 |
| MA0061.1 | 2.2047 |
| MA0063.1 | 0 |
| MA0066.1 | 0.736721 |
| MA0067.1 | 1.43651 |
| MA0068.1 | 0.247962 |
| MA0069.1 | 1.09737 |
| MA0070.1 | 1.08584 |
| MA0071.1 | 0.695094 |
| MA0072.1 | 1.0812 |
| MA0073.1 | 0.0140295 |
| MA0074.1 | 0.730989 |
| MA0076.1 | 1.33654 |
| MA0077.1 | 1.07324 |
| MA0078.1 | 0.836493 |
| MA0081.1 | 0.522409 |
| MA0083.1 | 1.12028 |
| MA0084.1 | 1.62584 |
| MA0087.1 | 1.07867 |
| MA0088.1 | 0.818263 |
| MA0089.1 | 0 |
| MA0090.1 | 0.556637 |
| MA0091.1 | 0.629594 |
| MA0092.1 | 0.588959 |
| MA0093.1 | 0.456342 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.750974 |
| MA0101.1 | 2.02769 |
| MA0103.1 | 0.442769 |
| MA0105.1 | 1.58771 |
| MA0106.1 | 0.779931 |
| MA0107.1 | 2.62998 |
| MA0108.2 | 0.94238 |
| MA0109.1 | 0 |
| MA0111.1 | 0.5713 |
| MA0113.1 | 0.797251 |
| MA0114.1 | 0.372523 |
| MA0115.1 | 1.35895 |
| MA0116.1 | 0.382106 |
| MA0117.1 | 1.1512 |
| MA0119.1 | 0.504689 |
| MA0122.1 | 1.17777 |
| MA0124.1 | 1.31673 |
| MA0125.1 | 1.23103 |
| MA0130.1 | 0 |
| MA0131.1 | 0.855546 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.14377 |
| MA0136.1 | 0.743749 |
| MA0139.1 | 0.277033 |
| MA0140.1 | 0.692258 |
| MA0141.1 | 0.520334 |
| MA0142.1 | 0.912455 |
| MA0143.1 | 0.797437 |
| MA0144.1 | 0.938075 |
| MA0145.1 | 0.143698 |
| MA0146.1 | 0.143081 |
| MA0147.1 | 0.386018 |
| MA0148.1 | 1.57313 |
| MA0149.1 | 0.681935 |
| MA0062.2 | 0.284987 |
| MA0035.2 | 0.691506 |
| MA0039.2 | 0.0118463 |
| MA0138.2 | 0.837782 |
| MA0002.2 | 0.30855 |
| MA0137.2 | 1.20193 |
| MA0104.2 | 0.320919 |
| MA0047.2 | 1.80892 |
| MA0112.2 | 0.136971 |
| MA0065.2 | 0.449243 |
| MA0150.1 | 0.550239 |
| MA0151.1 | 0 |
| MA0152.1 | 0.69926 |
| MA0153.1 | 1.21379 |
| MA0154.1 | 0.172764 |
| MA0155.1 | 0.409315 |
| MA0156.1 | 0.480289 |
| MA0157.1 | 0.883854 |
| MA0158.1 | 0 |
| MA0159.1 | 0.386729 |
| MA0160.1 | 0.669748 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0592265 |
| MA0163.1 | 0.0439995 |
| MA0164.1 | 0.810347 |
| MA0080.2 | 0.456437 |
| MA0018.2 | 0.781393 |
| MA0099.2 | 0.699641 |
| MA0079.2 | 0.0442129 |
| MA0102.2 | 1.66336 |
| MA0258.1 | 0.345771 |
| MA0259.1 | 0.395396 |
| 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 | 3 | 6.20641370047011 | 0.00777455012627559 | 0.0319545942793426 |
| E2F1#1869 | 4 | 3.92591137190346 | 0.00721498454710636 | 0.0298769188816955 |
| E2F4#1874 | 3 | 7.60083618917066 | 0.00435414736037571 | 0.020649477621028 |
| E2F6#1876 | 4 | 4.01372458535791 | 0.00663211823393388 | 0.0282945995193554 |
| ELF1#1997 | 4 | 3.40647836704603 | 0.0123506610529955 | 0.044733507532991 |
| EP300#2033 | 4 | 5.41915338097856 | 0.0020938692794389 | 0.0121166674243861 |
| FOXA1#3169 | 3 | 6.64885184963127 | 0.00638902516656872 | 0.0278084350644413 |
| GTF2B#2959 | 2 | 12.7775319737297 | 0.0091993608955972 | 0.0347878938581822 |
| HNF4G#3174 | 2 | 11.5013690105787 | 0.0112743830492105 | 0.0413791569889125 |
| IRF1#3659 | 4 | 6.10973100285112 | 0.00131552526476799 | 0.0088100123839118 |
| IRF3#3661 | 2 | 18.7927808845958 | 0.00433962977712151 | 0.0205890425790575 |
| JUND#3727 | 4 | 5.59573115349682 | 0.00184959330175546 | 0.0109339262377335 |
| MAFK#7975 | 2 | 10.840293255132 | 0.0126368327733788 | 0.0456876165063492 |
| MXI1#4601 | 3 | 5.97694297725558 | 0.00865300488936688 | 0.0329520939887179 |
| NANOG#79923 | 2 | 11.6979113924051 | 0.0109116495195608 | 0.040224551345643 |
| NFKB1#4790 | 5 | 5.48806342419384 | 0.000200816284746232 | 0.00239063626611327 |
| POU2F2#5452 | 3 | 5.46367443464551 | 0.0111565009446978 | 0.0410128054263741 |
| RFX5#5993 | 4 | 9.63832866175608 | 0.00022148012581572 | 0.00249661768592207 |
| SIN3A#25942 | 5 | 5.40888472681514 | 0.000215952267165727 | 0.00248062459640578 |
| SP1#6667 | 4 | 4.55870510251272 | 0.0040757356578168 | 0.0194848373325427 |
| SP2#6668 | 3 | 15.6921182963068 | 0.000527223591330277 | 0.0045634596929341 |
| ZNF143#7702 | 3 | 8.10052593133674 | 0.00362487051209098 | 0.018331292437162 |
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.
