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 5386 to 5435 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2693	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Divided	188.193	188.049	1.00077
2694	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
		Subtracted			0.142
2695	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]		144.412	144.553	0.141
	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	Divided	215.545	215.384	1.00075
2696	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
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Subtracted	144.411	144.552	0.141
2697	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144]	Divided	225.081	225.232	1.00067
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Subtracted	144.422	144.56	0.138
2698	transforming protein n-ras. [swissprot;acc:p01111]		144.427	144.564	0.137
	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Divided	188.435	188.31	1.00066
2699	calsyntenin-1 precursor. [swissprot;acc:o94985]
	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]	Subtracted	227.796	227.66	0.136
2700	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
	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]	Divided	188.435	188.31	1.00066
2701	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Subtracted	220.521	220.395	0.126
	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	Divided	216.539	216.682	1.00066
2702	importin 8; ran-binding protein 8. [refseq;acc:nm_006390]	Subtracted	220.521	220.395	0.126
	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	Divided	188.435	188.311	1.00066
2703	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]	Subtracted	220.521	220.395	0.126
	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Divided	188.435	188.311	1.00066
2704	gk001 protein. [refseq;acc:nm_020198]
	hsgcn1 (fragment). [sptrembl;acc:q99736]	Subtracted	220.521	220.395	0.126
2705	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]
	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	Divided	188.457	188.334	1.00065
2706	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]		188.459	188.336
	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Subtracted	188.435	188.31	0.125
2707	calsyntenin-1 precursor. [swissprot;acc:o94985]
	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]	Divided	215.096	215.232	1.00063
2708	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]		227.796	227.66	1.0006
	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]	Subtracted	188.435	188.31	0.125
2709	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Divided	220.521	220.395	1.00057
	similar to trna synthetase class ii. [refseq;acc:nm_152268]	Subtracted	220.224	220.348	0.124
2710	importin 8; ran-binding protein 8. [refseq;acc:nm_006390]	Divided	220.521	220.395	1.00057
	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	Subtracted	188.435	188.311	0.124
2711	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]	Divided	220.521	220.395	1.00057
	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Subtracted	188.435	188.311	0.124
2712	gk001 protein. [refseq;acc:nm_020198]
	hsgcn1 (fragment). [sptrembl;acc:q99736]	Divided	220.521	220.395	1.00057
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]
	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	Subtracted	188.457	188.334	0.123
2714	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]		188.459	188.336
	similar to trna synthetase class ii. [refseq;acc:nm_152268]	Divided	220.224	220.348	1.00056
2715	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]		216.018	215.903	1.00053
		Subtracted			0.115
2716	salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162]	Divided			1.00053
		Subtracted			0.115
2717	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Divided	216.521	216.634	1.00052
		Subtracted			0.113
2718	histidine-rich membrane protein ke4. [swissprot;acc:q92504]	Divided	216.52	216.632	1.00052

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.