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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 2680 to 2729 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
2680	HRAS	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	144.422	144.56	1.00096
2681	OTUB2	ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112]	203.592	203.787
2682	no value	transforming protein n-ras. [swissprot;acc:p01111]	144.427	144.564	1.00095
2683	YBX1	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]	208.438	208.635
2684	CSDA	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
2685	YBX2	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]
2686	PSMB7	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]	219.829	219.629	1.00091
2687	BCAT2	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382]	210.939	210.755	1.00087
2688	no value	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]	194.557	194.392	1.00085
2689	ACLY	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396]	213.792	213.619	1.00081
2690	AQP4	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	188.191	188.046	1.00077
2691	AQP2	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]	188.193	188.048
2692	AQP5	aquaporin 5. [swissprot;acc:p55064]	188.192
2693	MIP	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	188.193	188.049
2694	AQP1	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	188.223	188.081	1.00075
2695	SRP54	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	215.545	215.384
2696	ACO1	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]	201.652	201.794	1.0007
2697	ARPC2	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144]	225.081	225.232	1.00067
2698	SSR4	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	188.435	188.31	1.00066
2699	CLSTN1	calsyntenin-1 precursor. [swissprot;acc:o94985]
2700	no value	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	DCLK1	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	216.539	216.682
2702	PTPRB	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	188.435	188.311
2703	PRSS16	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]
2704	CCDC47	gk001 protein. [refseq;acc:nm_020198]
2705	CLSTN2	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	188.457	188.334	1.00065
2706	CLSTN3	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	188.459	188.336
2707	ACP1	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]	215.096	215.232	1.00063
2708	HMBS	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]	227.796	227.66	1.0006
2709	no value	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	220.521	220.395	1.00057
2710	IPO8	importin 8; ran-binding protein 8. [refseq;acc:nm_006390]
2711	ARFGEF2	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]
2712	GCN1L1	hsgcn1 (fragment). [sptrembl;acc:q99736]
2713	ARFGEF1	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	PARS2	similar to trna synthetase class ii. [refseq;acc:nm_152268]	220.224	220.348	1.00056
2715	no value	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	216.018	215.903	1.00053
2716	PRB4	salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162]
2717	MAPRE2	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	216.521	216.634	1.00052
2718	SLC39A7	histidine-rich membrane protein ke4. [swissprot;acc:q92504]	216.52	216.632
2719	MAPRE1	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]
2720	MAPRE3	microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]		216.633
2721	EPRS	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]	221.022	221.116	1.00043
2722	TBL2	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	219.308	219.214
2723	no value	lamin b2. [swissprot;acc:q03252]	219.323	219.413	1.00041
2724	HSP90AB1	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]	221.053	220.963
2725	DCX	doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	216.496	216.569	1.00034
2726	RAD17	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	221.001	220.927	1.00033
2727	no value	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	XRCC5	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	OTUB1	ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670]	202.123	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
- Hugo is the HGNC identifier if it exists
- 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.