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 6408 to 6457 of 7460 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2702	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
	microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]	Subtracted		216.633	0.113
2719	histidine-rich membrane protein ke4. [swissprot;acc:q92504]			216.632	0.112
	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]	Divided			1.00052
2720		Subtracted			0.112
	microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]	Divided		216.633	1.00052
2721	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
		Subtracted			0.094
2722	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	Divided	219.308	219.214	1.00043
		Subtracted			0.094
2723	lamin b2. [swissprot;acc:q03252]	Divided	219.323	219.413	1.00041
		Subtracted			0.09
2724	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]	Divided	221.053	220.963	1.00041
		Subtracted			0.09
2725	doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	Divided	216.496	216.569	1.00034
	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	Subtracted	221.001	220.927	0.074
2726	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]
	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	Divided			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]

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.