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	green	Filtered	Value Type	Interaction Map	Network Comparison Type	red	network_comparison

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Showing element 51 to 100 of 38536 in total

Network Comparison Type  : Divided

Rank	description	green	Filtered	Value Type	Interaction Map	red	network_comparison
4	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]	0.823905	0	Squared	Low confidence	0.00001	82390.5
	hbs1-like. [refseq;acc:nm_006620]	26.4292	1	Rooted	High confidence	50.9657	1.92839
		115.48		Squared		1596.92	13.8285
		698.5		Measured		2597.5	3.71868
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	9.43398	0	Rooted	Low confidence	0.00001	943398
		89		Measured			8900000
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]				High confidence
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	23.3131	1	Rooted	Low confidence	48.9847	2.10117
		69.9153		Squared		1362.75	19.4914
		543.5		Measured		2399.5	4.4149
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	0	Ranked	High confidence	8906	2.45711
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	20617			Low confidence	9607	2.14604
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	2.81207		Squared	High confidence	0.00001	281207
		10.4403		Rooted			1044030
5	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	0.00001		Squared	Low confidence	0.324024	32402.4
	cytohesin 4. [swissprot;acc:q9uia0]	28	1	Ranked	High confidence	15	1.86667
	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]	7.68115	0	Rooted	Low confidence	0.00001	768115
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479		Squared	High confidence		187479
		9.43398		Rooted			943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89		Measured			8900000
	jumonji protein. [swissprot;acc:q92833]	17.5166			Low confidence		1751660
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	18.4255	1	Rooted	High confidence	33.9632	1.84327
		27.2805		Squared		314.926	11.544
		339.5		Measured		1153.5	3.39764
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	330		Ranked	Low confidence	223	1.47982
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	45.9728		Rooted		27.1385	1.69401
		1057.25		Squared		128.386	8.23493
		2113.5		Measured		736.5	2.86965
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	0	Ranked	High confidence	5510.5	2.17144
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	19873			Low confidence	10889.4	1.82499
6	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	0.00001		Rooted		6.08276	608276
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]			Squared		0.324024	32402.4
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	28	1	Ranked	High confidence	15	1.86667
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	0	Measured		0.00001	8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479		Squared			187479
		9.43398		Rooted			943398
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001		Measured	Low confidence	13	1300000
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	18.4255	1	Rooted	High confidence	33.9632	1.84327
		27.2805		Squared		314.926	11.544
		339.5		Measured		1153.5	3.39764
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	45.9728		Rooted	Low confidence	27.1385	1.69401
		1057.25		Squared		128.386	8.23493
		2113.5		Measured		736.5	2.86965
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	240		Ranked		318	1.325
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	9583.37	0			5575.71	1.71877
	ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2			High confidence	7523	2.03897
7	cab2. [refseq;acc:nm_033419]	10950				21866	1.99689
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	0.00001		Rooted	Low confidence	6.08276	608276
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	6812		Ranked		11543	1.69451
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	1		High confidence	215	1.49767

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.