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

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

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

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.