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

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Showing element 1043 to 1092 of 3228 in total

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

Rank	description	red	green	network_comparison
1043	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7]	187.834	182.137	1.03128
1044	t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	173.475	178.889	1.03121
1045	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	115.817	119.432
1046	double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]	173.475	178.889
1047	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	187.022	181.391	1.03104
1048	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]	187.96	182.308	1.031
1049	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	211.449	217.998	1.03097
1050	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]
1051	17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
1052	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]
1053	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066]	207.04	200.84	1.03087
1054	60s ribosomal protein l21. [swissprot;acc:p46778]	223.958	217.263	1.03082
1055	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	219.01	212.468	1.03079
1056	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]
1057	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
1058	ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	228.105	221.293	1.03078
1059	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]
1060	nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	218.162	211.648
1061	elks protein. [refseq;acc:nm_015064]
1062	zinc finger protein 174 (aw-1). [swissprot;acc:q15697]	269.963	278.239	1.03066
1063	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	269.96	278.232	1.03064
1064	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	269.955	278.221	1.03062
1065	zinc finger protein 305. [swissprot;acc:o43309]	269.954	278.219
1066	zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022]	269.956	278.223
1067	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]
1068	zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6]	269.953	278.215	1.03061
1069	zinc finger protein 232. [swissprot;acc:q9uny5]	269.954	278.218
1070	zinc finger protein 99. [refseq;acc:nm_032164]
1071	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	231.277	238.356
1072	zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771]	269.954	278.217
1073	ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	216.901	210.485	1.03048
1074	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	174.387	179.697	1.03045
1075	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
1076	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
1077	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
1078	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
1079	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
1080	zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337]	269.896	278.093	1.03037
1081	40s ribosomal protein s30. [swissprot;acc:q05472]	223.44	216.875	1.03027
1082	phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613]	220.118	213.685	1.03011
1083	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]
1084	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]
1085	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	231.007	237.864	1.02968
1086	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	236.679	243.679	1.02958
1087	zinc finger protein 277. [swissprot;acc:q9nrm2]
1088	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995]	219.673	213.378	1.0295
1089	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	121.428	125.004	1.02945
1090	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	226.218	232.88
1091	block 23. [sptrembl;acc:q8nhw5]	226.205	232.858	1.02941
1092	60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388]	226.203	232.855

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.