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 51 to 100 of 3228 in total

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

description	Rank	red	green	network_comparison
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
40s ribosomal protein s26. [swissprot;acc:p02383]	1655	5488.7	5131.89	1.06953
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	2126	4806.33	5066.92	1.05422
40s ribosomal protein s28. [swissprot;acc:p25112]	700	7161.14	8015.92	1.11936
40s ribosomal protein s29. [swissprot;acc:p30054]	1756	3582.57	3357.6	1.067
40s ribosomal protein s3. [swissprot;acc:p23396]	2235	3674.29	3508.13	1.04736
40s ribosomal protein s30. [swissprot;acc:q05472]	1145	5893.97	6416.07	1.08858
40s ribosomal protein s3a. [swissprot;acc:p49241]	2263	4918.64	5145.39	1.0461
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	1974	3678.62	3470.64	1.05993
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	1967	3678.56	3470.55	1.05994
40s ribosomal protein s5. [swissprot;acc:p46782]	2343	3672.17	3516.98	1.04413
40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	1642	5782.92	6186.39	1.06977
40s ribosomal protein s8. [swissprot;acc:p09058]	1471	5659.45	6087.55	1.07564
40s ribosomal protein s9. [swissprot;acc:p46781]	2628	3933.74	3877.14	1.0146
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	2402	5078.5	5275.76	1.03884
43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]	1402	6160.06	6640.78	1.07804
44050 protein. [refseq;acc:nm_178832]	376	17385.9	14889.2	1.16769
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	972	7813.48	8570.11	1.09684
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	691	6920.69	7747.63	1.11949
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	689
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	688	6920.67	7747.6
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	687	6920.71	7747.65
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	686	6920.69	7747.63
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	692
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]	690
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126]	1606	5232.99	5606.53	1.07138
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	1229	5998.69	6509.74	1.08519

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.