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

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

Rank	network_comparison	description	green	Value Type	Interaction Map	red
1	2.55362	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	Ranked	Low confidence	5865
	3.70633	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915		High confidence	4294
	187479	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	Squared	Low confidence	0.00001
	716592	cab2. [refseq;acc:nm_033419]	7.16592		High confidence
	1907880	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	Rooted		19.0788
					Low confidence
	36400000			Measured	High confidence	364
					Low confidence
2	2.45711		21883	Ranked		8906
	2.55362	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977		High confidence	5865
	187479	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	Squared	Low confidence	0.00001
	561325	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001		High confidence	5.61325
	943398	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9.43398	Rooted	Low confidence	0.00001
	1240970	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001		High confidence	12.4097
	8900000	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	Measured	Low confidence	0.00001
	17400000	cab2. [refseq;acc:nm_033419]	174		High confidence
3	2.14604	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	Ranked	Low confidence	9607
	2.47638	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
	187479	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	Squared	Low confidence	0.00001
	561325	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001		High confidence	5.61325
	943398	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9.43398	Rooted	Low confidence	0.00001
	1240970	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001		High confidence	12.4097
	8900000	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	Measured	Low confidence	0.00001
	10900000	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109		High confidence
4	2.14604	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	20617	Ranked	Low confidence	9607
	2.45711	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883		High confidence	8906
	82390.5	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	Squared	Low confidence	0.00001
	281207	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	2.81207		High confidence
	943398	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	9.43398	Rooted	Low confidence
	1044030	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	10.4403		High confidence
	8900000	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	Measured	Low confidence
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]			High confidence
5	1.82499	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	19873	Ranked	Low confidence	10889.4
	2.17144	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7		High confidence	5510.5
	32402.4	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
	187479	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479		High confidence	0.00001
	768115	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	Rooted	Low confidence
	943398	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9.43398		High confidence
	1751660	jumonji protein. [swissprot;acc:q92833]	17.5166	Measured	Low confidence
	8900000	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89		High confidence
6	1.71877	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	9583.37	Ranked	Low confidence	5575.71
	2.03897	ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2		High confidence	7523
	32402.4	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	0.00001	Squared	Low confidence	0.324024
	187479	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479		High confidence	0.00001
	608276	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	Low confidence	6.08276
	943398	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9.43398		High confidence	0.00001
	1300000	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001	Measured	Low confidence	13
	8900000	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89		High confidence	0.00001
7	1.69451	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	Low confidence	11543
	1.99689	cab2. [refseq;acc:nm_033419]	10950		High confidence	21866

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.