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 4808 to 4857 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2404 cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Divided 5078.5 5275.76 1.03884
2405 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] Subtracted 4457.6 4642.72 185.12
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Divided 5078.5 5275.76 1.03884
2406 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Subtracted 3544.03 3359.43 184.6
2407 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Divided 5078.5 5275.76 1.03884
2408 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Subtracted 5454.62 5637.88 183.26
serpin b11. [swissprot;acc:q96p15] Divided 5078.5 5275.76 1.03884
2409 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Subtracted 4857.03 5039.78 182.75
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Divided 5078.5 5275.76 1.03884
2410 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Subtracted 4857.03 5039.78 182.75
2411 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Divided 5078.5 5275.76 1.03884
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Subtracted 4857.03 5039.78 182.75
2412 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 3936.2 3755.33 180.87
dynactin 4. [refseq;acc:nm_032486] Divided 4644.04 4470.47 1.03883
2413 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 6956.32 7223.14 1.03836
thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 3936.33 3755.5 180.83
2414 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] Divided 6956.32 7223.14 1.03836
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Subtracted 3641.62 3461.4 180.22
2415 60s ribosomal protein l5. [swissprot;acc:p46777] 3639.65 3459.64 180.01
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Divided 6956.62 7223.09 1.0383
2416 40s ribosomal protein s23. [swissprot;acc:p39028] Subtracted 3560.63 3381.34 179.29
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Divided 8048.38 7752.09 1.03822
2417 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Subtracted 3560.63 3381.34 179.29
60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Divided 3598.55 3467.65 1.03775
2418 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 4857.03 5039.78 1.03763
glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] Subtracted 6294.37 6472.9 178.53
2419 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 3641.4 3462.96 178.44
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Divided 4857.03 5039.78 1.03763
2420 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Subtracted 3641.45 3463.02 178.43
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Divided 4857.03 5039.78 1.03763
2421 60s ribosomal protein l23a. [swissprot;acc:p29316] Subtracted 3642.13 3463.88 178.25
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Divided 7355.46 7088.93 1.0376
2422 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Subtracted 8285.65 8107.49 178.16
2423 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 3569.06 3392.22 176.84
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Divided 7355.46 7088.93 1.0376
2424 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Subtracted 4418.21 4594.87 176.66
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Divided 7355.46 7088.93 1.0376
2425 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Subtracted 6562.71 6738.23 175.52
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Divided 7355.46 7088.93 1.0376
2426 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Subtracted 6562.71 6738.23 175.52
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Divided 6123.47 6351.84 1.03729
2427 dynactin 4. [refseq;acc:nm_032486] Subtracted 4644.04 4470.47 173.57
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Divided 5333.6 5531.41 1.03709
2428 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Subtracted 4164.76 4337.01 172.25
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Divided 7243.19 7509.81 1.03681
2429 60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted 3976.92 3804.85 172.07

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/