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

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Showing element 51 to 100 of 38536 in total

Network Comparison Type  : Divided

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

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.