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

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

Rank	description	Value Type	green	Interaction Map	red	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	15915	High confidence	4294	3.70633
	cab2. [refseq;acc:nm_033419]	Squared	7.16592		0.00001	716592
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		1.87479	Low confidence		187479
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	0.00001	High confidence	364	36400000
				Low confidence
		Rooted		High confidence	19.0788	1907880
				Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked	14977		5865	2.55362
2	cab2. [refseq;acc:nm_033419]	Measured	174	High confidence	0.00001	17400000
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89	Low confidence		8900000
		Rooted	9.43398			943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared	1.87479			187479
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked	21883		8906	2.45711
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		14977	High confidence	5865	2.55362
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	0.00001		5.61325	561325
		Rooted			12.4097	1240970
3	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	1.87479	Low confidence	0.00001	187479
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured	89			8900000
		Rooted	9.43398			943398
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Ranked	20617		9607	2.14604
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		11083.9	High confidence	4475.84	2.47638
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured	109		0.00001	10900000
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared	0.00001		5.61325	561325
		Rooted			12.4097	1240970
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]	Squared	0.823905	Low confidence	0.00001	82390.5
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	89			8900000
		Rooted	9.43398			943398
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	89	High confidence		8900000
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked	21883		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]	Squared	2.81207	High confidence	0.00001	281207
		Rooted	10.4403			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]	Squared	0.00001	Low confidence	0.324024	32402.4
	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]	Rooted	7.68115		0.00001	768115
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	1.87479	High confidence		187479
		Rooted	9.43398			943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured	89			8900000
	jumonji protein. [swissprot;acc:q92833]		17.5166	Low confidence		1751660
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Ranked	11965.7	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]	Rooted	0.00001		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
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	89	High confidence	0.00001	8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared	1.87479			187479
		Rooted	9.43398			943398
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Measured	0.00001	Low confidence	13	1300000
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Ranked	9583.37		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]	Rooted	0.00001	Low confidence	6.08276	608276

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.