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

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Showing element 27 to 76 of 3228 in total

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

description	Rank	network_comparison	red	green
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	2478	1.00289	216.177	216.801
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	2368	1.00402	218.555	219.434
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	2269	1.00556	217.419	218.627
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	2367	1.00407	217.589	218.475
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	2316	1.00493	217.241	218.311
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	2329	1.00462	217.112	218.116
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	1.00671	210.209	208.808
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	2440	1.00336	217.645	218.376
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	1.02028	220.987	225.468
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	2432	1.00347	215.807	216.556
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	2355	1.00428	217.232	218.162
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]	2525	1.00234	215.835	216.341
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	2620	1.00137	215.615	215.91
26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	2150	1.00686	217.871	219.366
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	810	1.04425	212.386	221.785
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	325	1.09941	243.944	268.195
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	2212	1.00643	224.411	225.854
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	23	1.31818	58	44
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]	1659	1.01443	217.925	214.826
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	2675	1.001	214.893	215.108
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	407	1.08673	239.75	260.544
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	3147	1	0.00001	0.00001
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	1.00509	191.567	192.542
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	1	0.00001	0.00001
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]	2189	1.00662	209.54	208.162
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	1852	1.01095	196.008	198.154
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	1.00511	191.563	192.541
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	1025	1.03195	205.632	199.266
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	1.03011	220.118	213.685
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	1.03882	272.878	283.472
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	2358	1.00423	198.181	197.346
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	1.01272	219.423	222.215
40s ribosomal protein s11. [swissprot;acc:p04643]	278	1.10642	241.399	267.088
40s ribosomal protein s13. [swissprot;acc:q02546]	1722	1.01319	220.899	223.813
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	386	1.09029	242.238	264.11
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	304	1.1017	242.339	266.986
40s ribosomal protein s15a. [swissprot;acc:p39027]	292	1.10357	241.411	266.414
40s ribosomal protein s16. [swissprot;acc:p17008]	391	1.09011	241.828	263.62
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	387	1.09029	242.238	264.11
40s ribosomal protein s19. [swissprot;acc:p39019]	861	1.04031	234.025	224.958
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	344	1.0973	241.625	265.136
40s ribosomal protein s20. [swissprot;acc:p17075]	342	1.09737	243.5	267.21
40s ribosomal protein s21. [swissprot;acc:p35265]	790	1.04578	224.244	234.511
40s ribosomal protein s23. [swissprot;acc:p39028]	324	1.09941	243.944	268.195
40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	1690	1.0138	224.091	227.184
40s ribosomal protein s26. [swissprot;acc:p02383]	454	1.07779	210.224	226.578
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	1102	1.02847	229.442	235.974

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.