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 4558 to 4607 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2279 transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Divided 191.936 190.909 1.00538
2280 epsin 3. [refseq;acc:nm_017957] Subtracted 218.153 219.284 1.131
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] Divided 212.793 211.657 1.00537
2281 splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] 219.652 218.482 1.00536
tripartite motif protein 2. [swissprot;acc:q9c040] Subtracted 202.312 203.437 1.125
2282 dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 207.319 208.44 1.121
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] Divided 219.652 218.482 1.00536
2283 proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] 212.81 211.676
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Subtracted 236.023 234.905 1.118
2284 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 161.547 162.665
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Divided 219.652 218.482 1.00536
2285 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Subtracted 217.392 218.498 1.106
splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368] Divided 219.652 218.482 1.00536
2286 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] Subtracted 217.392 218.498 1.106
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Divided 216.608 215.456 1.00535
2287 phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] 206.475 205.376
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] Subtracted 215.239 216.339 1.1
2288 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Divided 216.607 215.458 1.00533
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Subtracted 215.239 216.339 1.1
2289 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Divided 216.605 215.46 1.00531
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Subtracted 206.475 205.376 1.099
2290 myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Divided 200.158 201.213 1.00527
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

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/