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

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Showing element 1 to 50 of 3730 in total

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

description	Rank	network_comparison	red	green
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	242	1.09822	15260.6	13895.8
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]	47	1.42943	12941.7	18499.2
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	379	1.03909	11228.4	10806
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	495	1.00195	11725.2	11748.1
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	299	1.07178	12338.7	11512.3
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	327	1.05751	9897.29	10466.5
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	478	1.00854	10156.4	10243.1
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]	369	1.04536	18849.7	19704.7
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	222	1.10622	12183	11013.2
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	186	1.12672	11935.1	10592.8
40s ribosomal protein s26. [swissprot;acc:p02383]	112	1.1982	14269.7	17098
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	380	1.0387	9566.15	9936.37
40s ribosomal protein s28. [swissprot;acc:p25112]	258	1.09459	12967.1	14193.6
40s ribosomal protein s29. [swissprot;acc:p30054]	225	1.10378	11035.3	9997.71
40s ribosomal protein s3a. [swissprot;acc:p49241]	331	1.05644	10405.1	10992.4
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	261	1.09259	12448.9	11393.9
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	260	1.0926	12447.6	11392.6
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]	298	1.07219	11977.8	12842.5
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]	288	1.07517	14930.6	16053
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	412	1.03217	8546.06	8279.69
60s acidic ribosomal protein p1. [swissprot;acc:p05386]	233	1.1015	9586.97	10560
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	199	1.11721	11781.8	10545.7
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	397	1.03414	10006.9	9676.53
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	396	1.03436	10194.8	9856.12
60s ribosomal protein l12. [swissprot;acc:p30050]	394	1.0344	10196.9	9857.79
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	429	1.02539	12318.7	12631.5
60s ribosomal protein l15. [swissprot;acc:p39030]	188	1.12413	11745.2	13203.1
60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	277	1.08245	11096.8	10251.6
60s ribosomal protein l18a. [swissprot;acc:q02543]	102	1.22052	12738.7	10437.1
60s ribosomal protein l21. [swissprot;acc:p46778]	41	1.47871	9994.33	6758.83
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	411	1.0324	12115.7	12508.3
60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	311	1.06558	10253.5	9622.45
60s ribosomal protein l23a. [swissprot;acc:p29316]	205	1.11363	11844.9	10636.3
60s ribosomal protein l37a. [swissprot;acc:p12751]	46	1.42943	12941.7	18499.2
60s ribosomal protein l39. [swissprot;acc:p02404]	128	1.18073	11564.4	9794.29
60s ribosomal protein l7. [swissprot;acc:p18124]	147	1.16562	11080.3	9505.89
60s ribosomal protein l9. [swissprot;acc:p32969]	276	1.08257	10741.6	9922.33
acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	21	1.68236	6313.38	10621.4
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	382	1.03848	10449	10061.8
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]	105	1.21243	17410.5	14360
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]	368	1.04633	16679.2	15940.6
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]	402	1.03367	10562.4	10918
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	321	1.05864	11634.4	10989.9
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	498	1.00161	10231.8	10248.3
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	187	1.12641	9955.22	11213.7
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	259	1.09304	10438.3	9549.77
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	42	1.47509	8158	5530.5
adp-ribosylation factor 3. [swissprot;acc:p16587]	320	1.0611	11627.8	10958.2
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	1	3.70633	4294	15915
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	475	1.00903	18667	18500

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.