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	Filtered	Interaction Map	green	red	network_comparison

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Showing element 51 to 100 of 3228 in total

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

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