MK5 Microarray Data

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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Value Type	Gene	description	Rank	Interaction Map	Network Comparison Type	Filtered	red	green	network_comparison

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Showing element 32 to 81 of 3228 in total

Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1

description	Rank	red	green	network_comparison
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	2329	217.112	218.116	1.00462
26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200]	2175	210.209	208.808	1.00671
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	2440	217.645	218.376	1.00336
26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]	1432	220.987	225.468	1.02028
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	2432	215.807	216.556	1.00347
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	2355	217.232	218.162	1.00428
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]	2525	215.835	216.341	1.00234
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	2620	215.615	215.91	1.00137
26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	2150	217.871	219.366	1.00686
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	810	212.386	221.785	1.04425
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	325	243.944	268.195	1.09941
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	2212	224.411	225.854	1.00643
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	23	58	44	1.31818
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]	1659	217.925	214.826	1.01443
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	2675	214.893	215.108	1.001
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	407	239.75	260.544	1.08673
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	3147	0.00001	0.00001	1
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	2756
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060]	2802
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]	2303	191.567	192.542	1.00509
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714]	3180	0.00001	0.00001	1
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]	2189	209.54	208.162	1.00662
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	1852	196.008	198.154	1.01095
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	2300	191.563	192.541	1.00511
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	1025	205.632	199.266	1.03195
3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405]	1083	220.118	213.685	1.03011
3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213]	1084
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	897	272.878	283.472	1.03882
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	2358	198.181	197.346	1.00423
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	1745	219.423	222.215	1.01272
40s ribosomal protein s11. [swissprot;acc:p04643]	278	241.399	267.088	1.10642
40s ribosomal protein s13. [swissprot;acc:q02546]	1722	220.899	223.813	1.01319
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	386	242.238	264.11	1.09029
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	304	242.339	266.986	1.1017
40s ribosomal protein s15a. [swissprot;acc:p39027]	292	241.411	266.414	1.10357
40s ribosomal protein s16. [swissprot;acc:p17008]	391	241.828	263.62	1.09011
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	387	242.238	264.11	1.09029
40s ribosomal protein s19. [swissprot;acc:p39019]	861	234.025	224.958	1.04031
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	344	241.625	265.136	1.0973
40s ribosomal protein s20. [swissprot;acc:p17075]	342	243.5	267.21	1.09737
40s ribosomal protein s21. [swissprot;acc:p35265]	790	224.244	234.511	1.04578
40s ribosomal protein s23. [swissprot;acc:p39028]	324	243.944	268.195	1.09941
40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	1690	224.091	227.184	1.0138
40s ribosomal protein s26. [swissprot;acc:p02383]	454	210.224	226.578	1.07779
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	1102	229.442	235.974	1.02847
40s ribosomal protein s28. [swissprot;acc:p25112]	1982	200.343	198.427	1.00966
40s ribosomal protein s29. [swissprot;acc:p30054]	277	241.849	267.642	1.10665
40s ribosomal protein s3. [swissprot;acc:p23396]	346	241.612	265.119	1.09729
40s ribosomal protein s30. [swissprot;acc:q05472]	1081	223.44	216.875	1.03027
40s ribosomal protein s3a. [swissprot;acc:p49241]	867	225.689	234.674	1.03981

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.