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

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Showing element 25 to 74 of 3228 in total

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

description	Rank	red	green	network_comparison
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	1539	5783.97	6207.5	1.07322
26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]	2651	9150.44	9234.09	1.00914
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	1577	5923.66	6349.04	1.07181
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	1883	5826	6195.48	1.06342
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	1609	5826.74	6242.44	1.07134
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	1592	5853.1	6271.79	1.07153
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	1579	5842.44	6261.87	1.07179
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	1585	5858.48	6278.32	1.07166
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]	1241	6436.19	6980.13	1.08451
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	1546	5819.39	6244.37	1.07303
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]	1979	5475.74	5800.97	1.05939
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	1472	5984.47	6435.42	1.07535
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	1571	5851.64	6273.4	1.07208
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]	1536	5916.05	6350.53	1.07344
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	1517	5996.14	6439.46	1.07393
26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	1643	5782.92	6186.39	1.06977
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	2720	5603.24	5583.64	1.00351
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	2153	3560.63	3381.34	1.05302
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	1955	5195.3	5510.67	1.0607
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	115	21185	28492	1.34491
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]	835	5623.18	6218.77	1.10592
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	2071	6437.24	6797.24	1.05592
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	2530	3880.5	3788.42	1.02431
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]	2302	6946.6	7263.68	1.04565
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]	2105	6916.14	7295.24	1.05481
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	1898	6885.11	7317.48	1.0628
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	2305	6946.82	7263.87	1.04564
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	563	5480.24	6222.04	1.13536
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]	1274	5885	6371.14	1.08261
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]	1275
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	2547	3370.46	3444.18	1.02187
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	2261	6486.84	6786.23	1.04615
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]	1469	5473.09	5887.45	1.07571
40s ribosomal protein s11. [swissprot;acc:p04643]	1873	3618.46	3402.09	1.0636
40s ribosomal protein s13. [swissprot;acc:q02546]	1498	5414.98	5818.7	1.07456
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	2436	3708.67	3584.47	1.03465
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	2067	3602.75	3411.18	1.05616
40s ribosomal protein s15a. [swissprot;acc:p39027]	2008	3637.47	3435.61	1.05876
40s ribosomal protein s16. [swissprot;acc:p17008]	2448	3730.53	3611.05	1.03309
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	2437	3708.67	3584.47	1.03465
40s ribosomal protein s19. [swissprot;acc:p39019]	807	4708.61	5226.71	1.11003
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	2242	3670.45	3504.91	1.04723
40s ribosomal protein s20. [swissprot;acc:p17075]	2211	3590.56	3422.6	1.04907
40s ribosomal protein s21. [swissprot;acc:p35265]	2403	5078.5	5275.76	1.03884
40s ribosomal protein s23. [swissprot;acc:p39028]	2152	3560.63	3381.34	1.05302
40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	1599	5184.45	5554.97	1.07147

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.