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

Results: HTML CSV LaTeX

Showing element 6358 to 6407 of 7460 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
2677	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]	Subtracted	208.635	208.438	0.197
2678	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Divided	144.552	144.411	1.00098
2679	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]		189.959	190.142	1.00096
	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]	Subtracted	208.635	208.438	0.197
2680	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Divided	144.56	144.422	1.00096
	ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112]	Subtracted	203.787	203.592	0.195
2681	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382]		210.755	210.939	0.184
	ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112]	Divided	203.787	203.592	1.00096
2682	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]	Subtracted	189.959	190.142	0.183
	transforming protein n-ras. [swissprot;acc:p01111]	Divided	144.564	144.427	1.00095
2683	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396]	Subtracted	213.619	213.792	0.173
	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]	Divided	208.635	208.438	1.00095
2684	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
	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]	Subtracted	194.392	194.557	0.165
2685	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]	Divided	208.635	208.438	1.00095
	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	Subtracted	215.384	215.545	0.161
2686	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144]		225.232	225.081	0.151
	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]	Divided	219.629	219.829	1.00091
2687	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382]		210.755	210.939	1.00087
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Subtracted	144.538	144.391	0.147
2688	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]		188.046	188.191	0.145
	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]	Divided	194.392	194.557	1.00085
2689	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]	Subtracted	188.048	188.193	0.145
	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396]	Divided	213.619	213.792	1.00081
2690	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]		188.046	188.191	1.00077
	aquaporin 5. [swissprot;acc:p55064]	Subtracted	188.048	188.192	0.144
2691	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]	Divided		188.193	1.00077
	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Subtracted	188.049		0.144
2692	aquaporin 5. [swissprot;acc:p55064]	Divided	188.048	188.192	1.00077
	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	Subtracted	216.682	216.539	0.143
2693	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	201.652	0.142
	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Divided	188.049	188.193	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]		188.081	188.223	1.00075
		Subtracted			0.142
2695	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]		144.553	144.412	0.141
	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	Divided	215.384	215.545	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]		201.794	201.652	1.0007
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Subtracted	144.552	144.411	0.141
2697	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144]	Divided	225.232	225.081	1.00067
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Subtracted	144.56	144.422	0.138
2698	transforming protein n-ras. [swissprot;acc:p01111]		144.564	144.427	0.137
	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Divided	188.31	188.435	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	227.66	227.796	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]		215.232	215.096
	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	188.31	188.435	1.00066
2701	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Subtracted	220.395	220.521	0.126
	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	Divided	216.682	216.539	1.00066
2702	importin 8; ran-binding protein 8. [refseq;acc:nm_006390]	Subtracted	220.395	220.521	0.126

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.