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

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Showing element 51 to 100 of 3228 in total

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

description	green	Rank	red	network_comparison
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]	192.542	2303	191.567	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]	0.00001	3180	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]	208.162	2189	209.54	1.00662
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	198.154	1852	196.008	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]	192.541	2300	191.563	1.00511
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	199.266	1025	205.632	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]	213.685	1083	220.118	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]	283.472	897	272.878	1.03882
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	197.346	2358	198.181	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]	222.215	1745	219.423	1.01272
40s ribosomal protein s11. [swissprot;acc:p04643]	267.088	278	241.399	1.10642
40s ribosomal protein s13. [swissprot;acc:q02546]	223.813	1722	220.899	1.01319
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	264.11	386	242.238	1.09029
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	266.986	304	242.339	1.1017
40s ribosomal protein s15a. [swissprot;acc:p39027]	266.414	292	241.411	1.10357
40s ribosomal protein s16. [swissprot;acc:p17008]	263.62	391	241.828	1.09011
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	264.11	387	242.238	1.09029
40s ribosomal protein s19. [swissprot;acc:p39019]	224.958	861	234.025	1.04031
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	265.136	344	241.625	1.0973
40s ribosomal protein s20. [swissprot;acc:p17075]	267.21	342	243.5	1.09737
40s ribosomal protein s21. [swissprot;acc:p35265]	234.511	790	224.244	1.04578
40s ribosomal protein s23. [swissprot;acc:p39028]	268.195	324	243.944	1.09941
40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	227.184	1690	224.091	1.0138
40s ribosomal protein s26. [swissprot;acc:p02383]	226.578	454	210.224	1.07779
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	235.974	1102	229.442	1.02847
40s ribosomal protein s28. [swissprot;acc:p25112]	198.427	1982	200.343	1.00966
40s ribosomal protein s29. [swissprot;acc:p30054]	267.642	277	241.849	1.10665
40s ribosomal protein s3. [swissprot;acc:p23396]	265.119	346	241.612	1.09729
40s ribosomal protein s30. [swissprot;acc:q05472]	216.875	1081	223.44	1.03027
40s ribosomal protein s3a. [swissprot;acc:p49241]	234.674	867	225.689	1.03981
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	266.078	288	240.758	1.10517
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	266.079	287
40s ribosomal protein s5. [swissprot;acc:p46782]	265.756	366	242.473	1.09602
40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	219.366	2149	217.871	1.00686
40s ribosomal protein s8. [swissprot;acc:p09058]	214.049	1397	218.64	1.02145
40s ribosomal protein s9. [swissprot;acc:p46781]	257.784	439	238.986	1.07866
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]	234.511	789	224.244	1.04578
43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]	214.194	2232	215.547	1.00632
44050 protein. [refseq;acc:nm_178832]	151.009	2506	151.386	1.0025
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	207.862	2147	206.442	1.00688
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	203.954	879	212.002	1.03946
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]		877
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]		876
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]		875
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]		874
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]		880
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]		878
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126]	225.734	1769	223.016	1.01219
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]	214.409	1021	221.278	1.03204

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.