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	green	description	Network Comparison Type	Interaction Map	Value Type	network_comparison	red

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

Rank	green	description	Interaction Map	Value Type	network_comparison	red
1	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	Measured	36400000	364
				Rooted	1907880	19.0788
			Low confidence	Measured	36400000	364
				Rooted	1907880	19.0788
	1.87479	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Squared	187479	0.00001
	7.16592	cab2. [refseq;acc:nm_033419]	High confidence		716592
	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Low confidence	Ranked	2.55362	5865
	15915	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	High confidence		3.70633	4294
2	0.00001	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		Squared	561325	5.61325
				Rooted	1240970	12.4097
	1.87479	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Low confidence	Squared	187479	0.00001
	9.43398	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Rooted	943398
	89			Measured	8900000
	174	cab2. [refseq;acc:nm_033419]	High confidence		17400000
	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Ranked	2.55362	5865
	21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Low confidence		2.45711	8906
3	0.00001	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	High confidence	Squared	561325	5.61325
				Rooted	1240970	12.4097
	1.87479	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	Squared	187479	0.00001
	9.43398	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Rooted	943398
	89			Measured	8900000
	109	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence		10900000
	11083.9	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		Ranked	2.47638	4475.84
	20617	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence		2.14604	9607
4	0.823905	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	82390.5	0.00001
	2.81207	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence		281207
	9.43398	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	Rooted	943398
	10.4403	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence		1044030
	89	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	Measured	8900000
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence
	20617	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	Low confidence	Ranked	2.14604	9607
	21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence		2.45711	8906
5	0.00001	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Low confidence	Squared	32402.4	0.324024
	1.87479	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence		187479	0.00001
	7.68115	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]	Low confidence	Rooted	768115
	9.43398	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence		943398
	17.5166	jumonji protein. [swissprot;acc:q92833]	Low confidence	Measured	1751660
	89	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	High confidence		8900000
	11965.7	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]		Ranked	2.17144	5510.5
	19873	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence		1.82499	10889.4
6	0.00001	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]		Rooted	608276	6.08276
		carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		Squared	32402.4	0.324024
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		Measured	1300000	13
	1.87479	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	High confidence	Squared	187479	0.00001
	9.43398			Rooted	943398
	89	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		Measured	8900000
	9583.37	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Low confidence	Ranked	1.71877	5575.71
	15339.2	ubiquitin protein ligase. [refseq;acc:nm_130466]	High confidence		2.03897	7523
7	0.00001	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Low confidence	Rooted	608276	6.08276
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]		Measured	231962	2.31962

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.