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	green	Rank	network_comparison	Interaction Map	Network Comparison Type	red

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Showing element 1 to 50 of 14920 in total

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

description	green	Rank	network_comparison	red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	934.348	37	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]	26.1599	19	11.6763	305.45
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	2642.79	451	1.01545	2683.61
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	2263.85	474	1.00763	2281.12
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	5046.33	492	1.00159	5038.33
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	2853.65	438	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]	1721.76	346	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]	14.3333	121	1.3721	19.6667
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	1337.54	258	1.13048	1183.16
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	1735.23	222	1.15728	1499.4
40s ribosomal protein s26. [swissprot;acc:p02383]	81.2233	58	1.85588	150.741
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	2378.99	444	1.02223	2431.87
40s ribosomal protein s28. [swissprot;acc:p25112]	405.367	385	1.04615	387.486
40s ribosomal protein s29. [swissprot;acc:p30054]	1895.38	297	1.10737	1711.6
40s ribosomal protein s3a. [swissprot;acc:p49241]	2879.55	447	1.01735	2929.51
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	1495.22	255	1.1346	1317.84
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	1495.66	254	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]	1104.61	315	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]	142.417	57	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]	808.929	287	1.11385	726.245
60s acidic ribosomal protein p1. [swissprot;acc:p05386]	6739.34	313	1.09921	6131.07
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	1367.83	269	1.12309	1217.92
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	1771.04	322	1.09249	1621.1
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	1805.52	330	1.08882	1658.23
60s ribosomal protein l12. [swissprot;acc:p30050]	1805.05	328	1.08884	1657.78
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	219.891	392	1.04238	229.211
60s ribosomal protein l15. [swissprot;acc:p39030]	753.793	272	1.12261	846.216
60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	1906.28	232	1.14579	1663.73
60s ribosomal protein l18a. [swissprot;acc:q02543]	2604.71	419	1.03225	2688.7
60s ribosomal protein l21. [swissprot;acc:p46778]	992.083	72	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]	476.619	97	1.52879	728.65
60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	1956.36	284	1.11547	1753.85
60s ribosomal protein l23a. [swissprot;acc:p29316]	1463.51	259	1.1297	1295.49
60s ribosomal protein l37a. [swissprot;acc:p12751]	26.1599	18	11.6763	305.45
60s ribosomal protein l39. [swissprot;acc:p02404]	2923.92	412	1.03449	3024.78
60s ribosomal protein l7. [swissprot;acc:p18124]	2206.07	224	1.15183	1915.27
60s ribosomal protein l9. [swissprot;acc:p32969]	1894.01	265	1.12375	1685.44
acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	3340.03	177	1.23683	4131.06
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	739.623	378	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]	98.5074	44	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]	87.5499	60	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]	384.843	295	1.10902	426.8
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	2452.23	374	1.05527	2323.8
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	1591.6	347	1.06693	1491.75
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	1310.67	479	1.00587	1318.37
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	676.971	262	1.12926	764.479
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	1377	35	2.99674	459.5
adp-ribosylation factor 3. [swissprot;acc:p16587]	469.346	92	1.56086	300.697
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	47	13	29	1363
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	19	195	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.