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 2325 to 2374 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
green
network_comparison
2325 methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] 221.728 220.685 1.00473
2326 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] 220.076 219.05 1.00468
2327 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] 217.413 218.426 1.00466
2328 xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] 209.326 208.357 1.00465
2329 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] 217.112 218.116 1.00462
2330 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] 214.213 213.235 1.00459
2331 mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] 229.258 230.294 1.00452
2332 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]
2333 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
2334 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
2335 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
2336 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
2337 homeobox protein dlx-2. [swissprot;acc:q07687]
2338 homeobox protein dlx-5. [swissprot;acc:p56178]
2339 fetal brain protein 239 (239fb). [swissprot;acc:q15777]
2340 homeobox protein dlx-3. [swissprot;acc:o60479]
2341 activated p21cdc42hs kinase. [refseq;acc:nm_005781]
2342 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]
2343 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 212.222 211.27 1.00451
2344 kccr13l. [refseq;acc:nm_139179] 219.878 218.893 1.0045
2345 dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
2346 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 217.057 218.03 1.00448
2347 serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956]
2348 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
2349 fibulin-1 precursor. [swissprot;acc:p23142] 192.348 191.503 1.00441
2350 cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] 209.811 210.733 1.00439
2351 synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] 214.223 213.289 1.00438
2352 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] 215.088 214.155 1.00436
2353 electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] 182.232 183.027
2354 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] 215.078 214.148 1.00434
2355 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] 217.232 218.162 1.00428
2356 importin 4. [refseq;acc:nm_024658] 220.921 221.863 1.00426
2357 ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] 198.181 197.346 1.00423
2358 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
2359 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 207.196 208.056 1.00415
2360 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] 207.186 208.046
2361 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]
2362 phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] 207.178 208.037
2363 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] 207.186 208.046
2364 transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] 212.816 213.697 1.00414
2365 glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] 208.958 209.82 1.00413
2366 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 203.353 202.529 1.00407
2367 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] 217.589 218.475
2368 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] 218.555 219.434 1.00402
2369 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]
2370 ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]
2371 rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]
2372 mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] 212.724 213.574 1.004
2373 mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797]
2374 cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833]

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/