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

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Showing element 5908 to 5957 of 25824 in total

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

Rank	red	description	green	network_comparison
2680	144.422	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	144.56	1.00096
2681	203.592	ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112]	203.787
2682	144.427	transforming protein n-ras. [swissprot;acc:p01111]	144.564	1.00095
2683	208.438	nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991]	208.635
2684		dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
2685		germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]
2686	219.829	proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436]	219.629	1.00091
2687	210.939	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382]	210.755	1.00087
2688	194.557	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	194.392	1.00085
2689	213.792	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396]	213.619	1.00081
2690	188.191	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	188.046	1.00077
2691	188.193	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	188.048
2692	188.192	aquaporin 5. [swissprot;acc:p55064]
2693	188.193	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	188.049
2694	188.223	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	188.081	1.00075
2695	215.545	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	215.384
2696	201.652	iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399]	201.794	1.0007
2697	225.081	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144]	225.232	1.00067
2698	188.435	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	188.31	1.00066
2699		calsyntenin-1 precursor. [swissprot;acc:o94985]
2700		succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]
2701	216.539	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	216.682
2702	188.435	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	188.311
2703		thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]
2704		gk001 protein. [refseq;acc:nm_020198]
2705	188.457	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	188.334	1.00065
2706	188.459	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	188.336
2707	215.096	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]	215.232	1.00063
2708	227.796	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]	227.66	1.0006
2709	220.521	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	220.395	1.00057
2710		importin 8; ran-binding protein 8. [refseq;acc:nm_006390]
2711		brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]
2712		hsgcn1 (fragment). [sptrembl;acc:q99736]
2713		brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6]
2714	220.224	similar to trna synthetase class ii. [refseq;acc:nm_152268]	220.348	1.00056
2715	216.018	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	215.903	1.00053
2716		salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162]
2717	216.521	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	216.634	1.00052
2718	216.52	histidine-rich membrane protein ke4. [swissprot;acc:q92504]	216.632
2719		microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]
2720		microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]	216.633
2721	221.022	bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814]	221.116	1.00043
2722	219.308	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	219.214
2723	219.323	lamin b2. [swissprot;acc:q03252]	219.413	1.00041
2724	221.053	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]	220.963
2725	216.496	doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	216.569	1.00034
2726	221.001	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	220.927	1.00033
2727		atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]
2728		atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010]
2729	202.123	ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670]	202.06	1.00031

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.