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 4608 to 4657 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2304 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
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Subtracted 229.258 230.294 1.036
2316 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Divided 217.241 218.311 1.00493
homeobox protein dlx-3. [swissprot;acc:o60479] Subtracted 229.258 230.294 1.036
2317 activated p21cdc42hs kinase. [refseq;acc:nm_005781]
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Divided 194.834 195.794 1.00493
2318 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Subtracted 229.258 230.294 1.036
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Divided 194.834 195.794 1.00493
2319 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 194.842 195.8 1.00492
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Subtracted 191.936 190.909 1.027
2320 rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Divided 219.292 218.218 1.00492
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Subtracted 191.936 190.909 1.027
2321 tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Divided 203.909 202.925 1.00485
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Subtracted 191.936 190.909 1.027
2322 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 1.026
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Divided 236.023 234.905 1.00476
2323 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] Subtracted 217.413 218.426 1.013
asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Divided 192.773 193.691 1.00476
2324 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] Subtracted 217.112 218.116 1.004
proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] Divided 212.129 211.129 1.00474
2325 methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] 221.728 220.685 1.00473
proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] Subtracted 212.129 211.129 1
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] Divided 220.076 219.05 1.00468
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Subtracted 164.064 165.058 0.994
2327 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] Divided 217.413 218.426 1.00466
kccr13l. [refseq;acc:nm_139179] Subtracted 219.878 218.893 0.985
2328 dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Divided 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

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/