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

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Showing element 2325 to 2374 of 3228 in total

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

description	Rank	green	network_comparison	red
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	142	49	1.20408	59
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	141
ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410]	3112	0.00001	1	0.00001
ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]	2764
ras-related protein rab-1a (ypt1-related protein). [swissprot;acc:p11476]	2961
ras-related protein rab-1b. [swissprot;acc:q9h0u4]	2807
ras-related protein rab-26. [swissprot;acc:q9ulw5]	423	260.193	1.08284	240.287
ras-related protein rab-2a. [swissprot;acc:p08886]	3110	0.00001	1	0.00001
ras-related protein rab-37. [swissprot;acc:q96ax2]	422	260.193	1.08284	240.287
ras-related protein ral-a. [swissprot;acc:p11233]	3223	0.00001	1	0.00001
ras-related protein ral-b. [swissprot;acc:p11234]	2925
rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781]	3205
rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [refseq;acc:nm_005444]	2924
rd protein. [swissprot;acc:p18615]	238	254.15	1.11785	227.357
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626]	2006	222.971	1.00919	225.019
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860]	2008	222.969
receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303]	2004
recessive polycystic kidney disease protein tg737 homolog. [swissprot;acc:q13099]	3201	0.00001	1	0.00001
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666]	2707	215.232	1.00063	215.096
regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127]	1972	217.659	1.00973	219.777
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	2277	190.909	1.00538	191.936
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	159	298.263	1.19466	249.663
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	154
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	156
regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [swissprot;acc:q15714]	3114	0.00001	1	0.00001
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	402	226.218	1.08807	207.908
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]	401
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	1352	206.941	1.02209	211.513
rest corepressor. [refseq;acc:nm_015156]	1976	212.546	1.00972	214.611
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	2098	178.831	1.00741	177.515
reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799]	1461	211.077	1.0196	207.019
reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3]	1453	211.13	1.01976	207.038
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298]	1466	211.073	1.01957	207.022
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197]	1469	211.05	1.0195	207.013
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329]	2224	220.108	1.00637	221.509
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	687	125.389	1.05602	132.413
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	1012	210.185	1.03252	217.021
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	1011	210.189	1.03253	217.026
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338]	1216	212.918	1.02513	218.269
retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]	2759	0.00001	1	0.00001
retinoic acid receptor rxr-beta. [swissprot;acc:p28702]	3067
retinoic acid receptor rxr-gamma. [swissprot;acc:p48443]	2936
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]	1052	217.998	1.03097	211.449
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	187	198.444	1.14179	226.582
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	353	211.252	1.09694	231.73
rh type c glycoprotein. [refseq;acc:nm_016321]	1916	198.88	1.01016	196.88
rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407]	1926	198.91	1.01008	196.925
rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094]	1927	198.914	1.01006	196.932
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]	786	233.508	1.04685	244.447
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320]	1777	214.286	1.0121	216.878

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.