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

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Showing element 1 to 50 of 3228 in total

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

description	Rank	green	network_comparison	red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	60	2765.82	1.6231	4489.19
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	509	8630.06	1.14278	7551.8
1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	508	8636.87	1.14293	7556.75
1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]	514	8532.02	1.1411	7477
1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7]	513	8543.66	1.14143	7485.08
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147]	3126	0.00001	1	0.00001
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	1136	6303.92	1.08864	5790.65
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	2922	0.00001	1	0.00001
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	1411	6262.07	1.07743	5812.02
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655]	3088	0.00001	1	0.00001
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	1415	6265.44	1.0774	5815.33
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	1600	6788.96	1.07145	6336.22
15 kda selenoprotein precursor. [swissprot;acc:o60613]	1043	6933.36	1.09283	6344.41
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]	2855	0.00001	1	0.00001
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]	2521	6113.96	1.02511	5964.17
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]	1393	6192.72	1.07824	5743.36
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218]	2506	6362.25	1.0261	6200.39
2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]	2451	6957.34	1.03268	6737.15
2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953]	2288	6048.94	1.04585	5783.76
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	107	5843.51	1.36977	4266.04
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	3079	0.00001	1	0.00001
26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]	1521	6376.76	1.07379	5938.56
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	1527	6362.33	1.07349	5926.76
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	1567	6242.94	1.07226	5822.25
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	1539	6207.5	1.07322	5783.97
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	9234.09	1.00914	9150.44
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	1577	6349.04	1.07181	5923.66
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	1883	6195.48	1.06342	5826
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	1609	6242.44	1.07134	5826.74
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	1592	6271.79	1.07153	5853.1
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	1579	6261.87	1.07179	5842.44
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	1585	6278.32	1.07166	5858.48
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	6980.13	1.08451	6436.19
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	1546	6244.37	1.07303	5819.39
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	5800.97	1.05939	5475.74
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	1472	6435.42	1.07535	5984.47
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	1571	6273.4	1.07208	5851.64
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]	1536	6350.53	1.07344	5916.05
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	1517	6439.46	1.07393	5996.14
26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	1643	6186.39	1.06977	5782.92
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	2720	5583.64	1.00351	5603.24
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	2153	3381.34	1.05302	3560.63
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	1955	5510.67	1.0607	5195.3
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	115	28492	1.34491	21185
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]	835	6218.77	1.10592	5623.18
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	2071	6797.24	1.05592	6437.24
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	2530	3788.42	1.02431	3880.5
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	3147	0.00001	1	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

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.