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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red 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
green
red
network_comparison
2329 tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Subtracted 202.925 203.909 0.984
2330 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Divided 213.235 214.213 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] 192.541 191.563
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Divided 230.294 229.258 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 192.542 191.567 0.975
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Divided 230.294 229.258 1.00452
2333 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Subtracted 192.542 191.567 0.975
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Divided 230.294 229.258 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 192.542 191.567 0.975
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Divided 230.294 229.258 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 218.03 217.057 0.973
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Divided 230.294 229.258 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 218.03 217.057 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 230.294 229.258 1.00452
2338 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Subtracted 192.544 191.571 0.973
homeobox protein dlx-5. [swissprot;acc:p56178] Divided 230.294 229.258 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 208.357 209.326 0.969
2340 homeobox protein dlx-3. [swissprot;acc:o60479] Divided 230.294 229.258 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 195.708 194.743 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] 195.787 194.825 0.962
activated p21cdc42hs kinase. [refseq;acc:nm_005781] Divided 230.294 229.258 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 195.794 194.834 0.96
2343 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Divided 211.27 212.222 1.00451
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Subtracted 195.794 194.834 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] 195.8 194.842 0.958
kccr13l. [refseq;acc:nm_139179] Divided 218.893 219.878 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 211.27 212.222 0.952
2346 importin 4. [refseq;acc:nm_024658] 221.863 220.921 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 218.03 217.057 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 213.289 214.223 0.934
2348 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] 214.155 215.088 0.933
glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Divided 218.03 217.057 1.00448
2349 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] Subtracted 214.148 215.078 0.93
fibulin-1 precursor. [swissprot;acc:p23142] Divided 191.503 192.348 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 218.162 217.232 0.93
cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Divided 210.733 209.811 1.00439
2351 Subtracted 0.922
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Divided 213.289 214.223 1.00438
2352 asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Subtracted 193.691 192.773 0.918
copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] Divided 214.155 215.088 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 218.475 217.589 0.886
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Divided 183.027 182.232 1.00436
2354 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] 214.148 215.078 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/