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	green	red	network_comparison

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Showing element 6408 to 6457 of 7460 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
2702	dynein light chain 2. [refseq;acc:nm_080677]	Subtracted	5260	5239.33	20.67
2703	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Divided	9007.71	8972.87	1.00388
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Subtracted	10163.6	10143.6	20
2704	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]	Divided	9013.33	8980.12	1.0037
	testis-specific protein tex28. [swissprot;acc:o15482]	Subtracted	5583.64	5603.24	19.6
2705	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	Divided	4152.72	4137.61	1.00365
	similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]	Subtracted	5583.64	5603.24	19.6
2706	a kindred of iglon. [refseq;acc:nm_173808]
	peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347]	Divided	9012.31	8979.61	1.00364
2707	ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]	Subtracted	5583.64	5603.24	19.6
	prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675]	Divided	9012.31	8979.61	1.00364
2708	inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]	Subtracted	5583.64	5603.24	19.6
	j domain protein c21orf55. [swissprot;acc:q9nx36]	Divided	9012.42	8979.78	1.00363
2709	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	Subtracted	5583.64	5603.24	19.6
	testis-specific protein tex28. [swissprot;acc:o15482]	Divided			1.00351
2710	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]	Subtracted			19.6
	similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]	Divided			1.00351
2711	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]		5351.72	5332.98
	syntaxin 16 (syn16). [swissprot;acc:o14662]	Subtracted	5583.64	5603.24	19.6
2712	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
	a kindred of iglon. [refseq;acc:nm_173808]	Divided			1.00351
2713	ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Subtracted			19.6
2714	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
	inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]	Divided			1.00351
2715	adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]	Subtracted			19.6
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Divided	5351.72	5332.98	1.00351
2716	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]
	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	Subtracted	5583.64	5603.24	19.6
2717	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	Divided			1.00351
	syntaxin 1b. [swissprot;acc:q15531]	Subtracted			19.6
2718	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]	Divided			1.00351
	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	Subtracted			19.6
2719	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
	syntaxin 16 (syn16). [swissprot;acc:o14662]	Divided			1.00351
2720	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	Subtracted	3972.32	3953.53	18.79
2721	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Divided	5583.64	5603.24	1.00351
2722	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]	Subtracted	3972.32	3953.53	18.79
2723	adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]	Divided	5583.64	5603.24	1.00351
	oligophrenin 1. [swissprot;acc:o60890]	Subtracted	3972.32	3953.53	18.79
2724	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]		5351.72	5332.98	18.74
	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	Divided	5583.64	5603.24	1.00351
2725	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Subtracted	5351.72	5332.98	18.74
	syntaxin 1b. [swissprot;acc:q15531]	Divided	5583.64	5603.24	1.00351
2726	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]		5351.72	5332.98
	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]	Subtracted			18.74
2727	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]

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.