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

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Showing element 901 to 950 of 77072 in total

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green	red	description	Rank	Interaction Map	Value Type	network_comparison	Network Comparison Type
10.7125	9.16047	40s ribosomal protein s17. [swissprot;acc:p08708]	151	Low confidence	Rooted	1.16943	Divided
			454			1.55203	Subtracted
10.7395	11.5912	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	411			1.07931	Divided
			619			0.8517	Subtracted
10.8929	16.237	dead-box protein. [refseq;acc:nm_018665]	57	High confidence		1.4906	Divided
			87			5.3441	Subtracted
10.958	13.9573	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	108	Low confidence		1.27371	Divided
			274			2.9993	Subtracted
11.0968	10.5792	proactivator polypeptide precursor [contains: saposin a (protein a); saposin b (sphingolipid activator protein 1) (sap-1) (cerebroside sulfate activator) (csact) (dispersin) (sulfatide/gm1 activator); saposin c (co-beta-glucosidase) (a1 activator) (glucosylceramidase activator) (sphingolipid activator protein 2) (sap-2); saposin d (protein c) (component c)]. [swissprot;acc:p07602]	533			1.04893	Divided
			697			0.5176	Subtracted
11.2174	14.7289	metaxin 1. [swissprot;acc:q13505]	95	High confidence		1.31304	Divided
			155			3.5115	Subtracted
11.258	24.0391	ubiquitin protein ligase. [refseq;acc:nm_130466]	15			12.7811
			32			2.13529	Divided
11.4841	13.586	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	140	Low confidence		1.18303
			357			2.1019	Subtracted
11.4842	13.5864	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	139			1.18305	Divided
			356			2.1022	Subtracted
11.4844	13.5862	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	141			1.18301	Divided
			358			2.1018	Subtracted
11.4849	9.1258	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	118	High confidence		1.25851	Divided
			247			2.3591	Subtracted
11.5	14	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	176	Low confidence	Measured	1.21739	Divided
			190	High confidence
			489			2.5	Subtracted
			819	Low confidence
11.5571	12.3602	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	444		Rooted	1.06949	Divided
			628			0.8031	Subtracted
		ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	445			1.06949	Divided
			629			0.8031	Subtracted
11.6055	12.8769	neurocalcin delta. [swissprot;acc:p29554]	247	High confidence		1.10955	Divided
			337			1.2714	Subtracted
11.7898	23.8747	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	12	Low confidence		12.0849
			20	High confidence
			24	Low confidence		2.02503	Divided
			35	High confidence
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	19			12.0849	Subtracted
			34			2.02503	Divided
11.824	13.8773	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	152			1.17366
			273			2.0533	Subtracted
11.8643	13.9593	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	146			1.17658	Divided
			268			2.095	Subtracted
11.8854	12.7534	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	301			1.07303	Divided
			390			0.868	Subtracted
11.9458	8.7827	sedlin. [swissprot;acc:o14582]	74	Low confidence		1.36015	Divided
			265			3.1631	Subtracted
12	10	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	134	High confidence		1.2	Divided
			279			2	Subtracted
	13.6748	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	207			1.13957	Divided
			300			1.6748	Subtracted

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.