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

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Showing element 1 to 50 of 14920 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence

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]	37	934.348	2.79409	334.401
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]	19	26.1599	11.6763	305.45
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	451	2642.79	1.01545	2683.61
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	474	2263.85	1.00763	2281.12
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	492	5046.33	1.00159	5038.33
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	438	2853.65	1.0252	2925.57
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	346	1721.76	1.06708	1837.26
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]	121	14.3333	1.3721	19.6667
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	258	1337.54	1.13048	1183.16
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	222	1735.23	1.15728	1499.4
40s ribosomal protein s26. [swissprot;acc:p02383]	58	81.2233	1.85588	150.741
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	444	2378.99	1.02223	2431.87
40s ribosomal protein s28. [swissprot;acc:p25112]	385	405.367	1.04615	387.486
40s ribosomal protein s29. [swissprot;acc:p30054]	297	1895.38	1.10737	1711.6
40s ribosomal protein s3a. [swissprot;acc:p49241]	447	2879.55	1.01735	2929.51
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	255	1495.22	1.1346	1317.84
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	254	1495.66	1.13461	1318.22
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]	315	1104.61	1.09796	1212.82
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]	57	142.417	1.89769	270.264
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	287	808.929	1.11385	726.245
60s acidic ribosomal protein p1. [swissprot;acc:p05386]	313	6739.34	1.09921	6131.07
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	269	1367.83	1.12309	1217.92
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	322	1771.04	1.09249	1621.1
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	330	1805.52	1.08882	1658.23
60s ribosomal protein l12. [swissprot;acc:p30050]	328	1805.05	1.08884	1657.78
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	392	219.891	1.04238	229.211
60s ribosomal protein l15. [swissprot;acc:p39030]	272	753.793	1.12261	846.216
60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	232	1906.28	1.14579	1663.73
60s ribosomal protein l18a. [swissprot;acc:q02543]	419	2604.71	1.03225	2688.7
60s ribosomal protein l21. [swissprot;acc:p46778]	72	992.083	1.73441	572
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	97	476.619	1.52879	728.65
60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	284	1956.36	1.11547	1753.85
60s ribosomal protein l23a. [swissprot;acc:p29316]	259	1463.51	1.1297	1295.49
60s ribosomal protein l37a. [swissprot;acc:p12751]	18	26.1599	11.6763	305.45
60s ribosomal protein l39. [swissprot;acc:p02404]	412	2923.92	1.03449	3024.78
60s ribosomal protein l7. [swissprot;acc:p18124]	224	2206.07	1.15183	1915.27
60s ribosomal protein l9. [swissprot;acc:p32969]	265	1894.01	1.12375	1685.44
acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	177	3340.03	1.23683	4131.06
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	378	739.623	1.05199	703.068
acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	44	98.5074	2.16837	45.4292
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	60	87.5499	1.8441	47.4756
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	295	384.843	1.10902	426.8
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	374	2452.23	1.05527	2323.8
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	347	1591.6	1.06693	1491.75
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	479	1310.67	1.00587	1318.37
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	262	676.971	1.12926	764.479
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	35	1377	2.99674	459.5
adp-ribosylation factor 3. [swissprot;acc:p16587]	92	469.346	1.56086	300.697
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	13	47	29	1363
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	195	19	1.21053	23

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.