Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4580 to 4629 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2290 pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Subtracted 181.091 179.999 1.092
2291 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Divided 200.158 201.213 1.00527
ubiquitin. [swissprot;acc:p02248] Subtracted 216.617 215.529 1.088
2292 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 215.554 214.467 1.087
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Divided 200.158 201.213 1.00527
2293 large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379]
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Subtracted 215.543 214.459 1.084
2294 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 215.542 1.083
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Divided 162.331 163.187 1.00527
2295 camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Subtracted 215.542 214.459 1.083
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Divided 162.86 163.712 1.00523
2296 camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Subtracted 215.542 214.459 1.083
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Divided 206.451 205.38 1.00521
2297 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] Subtracted 215.529 214.449 1.08
epsin 3. [refseq;acc:nm_017957] Divided 218.153 219.284 1.00518
2298 rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Subtracted 219.292 218.218 1.074
ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] Divided 215.239 216.339 1.00511
2299 phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Subtracted 206.451 205.38 1.071
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Divided 215.239 216.339 1.00511
2300 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Subtracted 217.241 218.311 1.07
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Divided 191.563 192.541 1.00511
2301 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] 217.392 218.498 1.00509
symplekin. [swissprot;acc:q92797] Subtracted 162.741 163.8 1.059
2302 hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] Divided 191.567 192.542 1.00509
myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Subtracted 200.158 201.213 1.055
2303 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Divided 191.567 192.542 1.00509
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Subtracted 200.158 201.213 1.055
2304 hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Divided 191.567 192.542 1.00509
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Subtracted 200.158 201.213 1.055
2305 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Divided 217.392 218.498 1.00509
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Subtracted 200.158 201.213 1.055
2306 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Divided 191.571 192.544 1.00508
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Subtracted 221.728 220.685 1.043
2307 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] Divided 215.554 214.467 1.00507
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Subtracted 229.258 230.294 1.036
2308 protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Divided 215.543 214.459 1.00505
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Subtracted 229.258 230.294 1.036
2309 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Divided 215.542 214.459 1.00505
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Subtracted 229.258 230.294 1.036
2310 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
ubiquitin. [swissprot;acc:p02248] Divided 216.617 215.529 1.00505
2311 camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 215.542 214.459
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Subtracted 229.258 230.294 1.036
2312 camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Divided 215.542 214.459 1.00505
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Subtracted 229.258 230.294 1.036
2313 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] Divided 215.529 214.449 1.00504
homeobox protein dlx-2. [swissprot;acc:q07687] Subtracted 229.258 230.294 1.036
2314 homeobox protein dlx-5. [swissprot;acc:p56178]
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Divided 194.743 195.708 1.00496
2315 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 194.825 195.787 1.00494

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/