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

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Showing element 51 to 100 of 38536 in total

Network Comparison Type  : Divided

Rank	Value Type	description	Interaction Map	Filtered	red	green	network_comparison
4	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence	0	0.00001	89	8900000
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	1	2399.5	543.5	4.4149
	Ranked	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]			223	330	1.47982
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	High confidence		15	28	1.86667
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		0	8906	21883	2.45711
		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	Low confidence		9607	20617	2.14604
	Squared	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]			0.00001	0.823905	82390.5
		hbs1-like. [refseq;acc:nm_006620]	High confidence	1	1596.92	115.48	13.8285
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence		1362.75	69.9153	19.4914
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence	0	0.00001	2.81207	281207
	Rooted	hbs1-like. [refseq;acc:nm_006620]		1	50.9657	26.4292	1.92839
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	0	0.00001	9.43398	943398
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]		1	48.9847	23.3131	2.10117
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence	0	0.00001	10.4403	1044030
5	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]				89	8900000
		jumonji protein. [swissprot;acc:q92833]	Low confidence			17.5166	1751660
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	High confidence	1	1153.5	339.5	3.39764
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence		736.5	2113.5	2.86965
	Ranked	cytohesin 4. [swissprot;acc:q9uia0]	High confidence		15	28	1.86667
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence		223	330	1.47982
		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	High confidence	0	5510.5	11965.7	2.17144
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence		10889.4	19873	1.82499
	Squared	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]			0.324024	0.00001	32402.4
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence		0.00001	1.87479	187479
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		1	314.926	27.2805	11.544
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence		128.386	1057.25	8.23493
	Rooted	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]		0	0.00001	7.68115	768115
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence			9.43398	943398
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		1	33.9632	18.4255	1.84327
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence		27.1385	45.9728	1.69401
6	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	High confidence	0	0.00001	89	8900000
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence		13	0.00001	1300000
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	High confidence	1	1153.5	339.5	3.39764
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence		736.5	2113.5	2.86965
	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	High confidence		15	28	1.86667
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence		318	240	1.325
		trinucleotide repeat containing 15. [refseq;acc:nm_015575]		0	5575.71	9583.37	1.71877
		ubiquitin protein ligase. [refseq;acc:nm_130466]	High confidence		7523	15339.2	2.03897
	Squared	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Low confidence		0.324024	0.00001	32402.4
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	High confidence		0.00001	1.87479	187479
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		1	314.926	27.2805	11.544
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence		128.386	1057.25	8.23493
	Rooted	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]		0	6.08276	0.00001	608276
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	High confidence		0.00001	9.43398	943398
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		1	33.9632	18.4255	1.84327
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence		27.1385	45.9728	1.69401
7	Measured	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]			736.5	2113.5	2.86965
		sedlin. [swissprot;acc:o14582]	High confidence	0	0.00001	43	4300000
		sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]		1	1153.5	339.5	3.39764
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Low confidence	0	2.31962	0.00001	231962

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.