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 4658 to 4707 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2329 tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Subtracted 203.909 202.925 0.984
2330 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Divided 214.213 213.235 1.00459
Subtracted 0.978
2331 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 191.563 192.541
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Divided 229.258 230.294 1.00452
2332 hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] Subtracted 191.567 192.542 0.975
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Divided 229.258 230.294 1.00452
2333 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Subtracted 191.567 192.542 0.975
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Divided 229.258 230.294 1.00452
2334 hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Subtracted 191.567 192.542 0.975
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Divided 229.258 230.294 1.00452
2335 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Subtracted 217.057 218.03 0.973
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Divided 229.258 230.294 1.00452
2336 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] Subtracted 217.057 218.03 0.973
2337 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
homeobox protein dlx-2. [swissprot;acc:q07687] Divided 229.258 230.294 1.00452
2338 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Subtracted 191.571 192.544 0.973
homeobox protein dlx-5. [swissprot;acc:p56178] Divided 229.258 230.294 1.00452
2339 fetal brain protein 239 (239fb). [swissprot;acc:q15777]
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Subtracted 209.326 208.357 0.969
2340 homeobox protein dlx-3. [swissprot;acc:o60479] Divided 229.258 230.294 1.00452
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] Subtracted 194.743 195.708 0.965
2341 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 0.962
activated p21cdc42hs kinase. [refseq;acc:nm_005781] Divided 229.258 230.294 1.00452
2342 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Subtracted 194.834 195.794 0.96
2343 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Divided 212.222 211.27 1.00451
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Subtracted 194.834 195.794 0.96
2344 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 0.958
kccr13l. [refseq;acc:nm_139179] Divided 219.878 218.893 1.0045
2345 dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Subtracted 212.222 211.27 0.952
2346 importin 4. [refseq;acc:nm_024658] 220.921 221.863 0.942
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Divided 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]
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Subtracted 214.223 213.289 0.934
2348 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] 215.088 214.155 0.933
glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Divided 217.057 218.03 1.00448
2349 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] Subtracted 215.078 214.148 0.93
fibulin-1 precursor. [swissprot;acc:p23142] Divided 192.348 191.503 1.00441
2350 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] Subtracted 217.232 218.162 0.93
cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Divided 209.811 210.733 1.00439
2351 Subtracted 0.922
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Divided 214.223 213.289 1.00438
2352 asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Subtracted 192.773 193.691 0.918
copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] Divided 215.088 214.155 1.00436
2353 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] Subtracted 217.589 218.475 0.886
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Divided 182.232 183.027 1.00436
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

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/