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	Network Comparison Type	network_comparison	Value Type	green	red	Interaction Map

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

Rank	description	network_comparison	Value Type	green	red	Interaction Map
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	3.70633	Ranked	15915	4294	High confidence
	cab2. [refseq;acc:nm_033419]	716592	Squared	7.16592	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	187479		1.87479		Low confidence
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	1907880	Rooted	0.00001	19.0788	High confidence
						Low confidence
		36400000	Measured		364	High confidence
						Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	2.55362	Ranked	14977	5865
2	cab2. [refseq;acc:nm_033419]	17400000	Measured	174	0.00001	High confidence
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	943398	Rooted	9.43398		Low confidence
		8900000	Measured	89
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	187479	Squared	1.87479
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	2.45711	Ranked	21883	8906
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	2.55362		14977	5865	High confidence
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	561325	Squared	0.00001	5.61325
		1240970	Rooted		12.4097
3	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	187479	Squared	1.87479	0.00001	Low confidence
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	943398	Rooted	9.43398
		8900000	Measured	89
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	2.14604	Ranked	20617	9607
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	2.47638		11083.9	4475.84	High confidence
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	10900000	Measured	109	0.00001
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	561325	Squared	0.00001	5.61325
		1240970	Rooted		12.4097
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]	82390.5	Squared	0.823905	0.00001	Low confidence
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	943398	Rooted	9.43398
		8900000	Measured	89
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]					High confidence
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	2.45711	Ranked	21883	8906
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	2.14604		20617	9607	Low confidence
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	281207	Squared	2.81207	0.00001	High confidence
		1044030	Rooted	10.4403
5	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	Squared	0.00001	0.324024	Low confidence
	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	Rooted	7.68115	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	187479	Squared	1.87479		High confidence
		943398	Rooted	9.43398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	8900000	Measured	89
	jumonji protein. [swissprot;acc:q92833]	1751660		17.5166		Low confidence
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	2.17144	Ranked	11965.7	5510.5	High confidence
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	1.82499		19873	10889.4	Low confidence
6	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	608276	Rooted	0.00001	6.08276
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	32402.4	Squared		0.324024
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	8900000	Measured	89	0.00001	High confidence
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	187479	Squared	1.87479
		943398	Rooted	9.43398
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	1300000	Measured	0.00001	13	Low confidence
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	1.71877	Ranked	9583.37	5575.71
	ubiquitin protein ligase. [refseq;acc:nm_130466]	2.03897		15339.2	7523	High confidence
7	cab2. [refseq;acc:nm_033419]	1.99689		10950	21866
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	608276	Rooted	0.00001	6.08276	Low confidence

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.