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