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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

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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	Interaction Map	red
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	3.70633	Ranked	15915	High confidence	4294
	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	High confidence	19.0788
					Low confidence
		36400000	Measured		High confidence	364
					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	High confidence	0.00001
	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	High confidence	5865
	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	Low confidence	0.00001
	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	High confidence	4475.84
	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	Low confidence	0.00001
	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	Low confidence	9607
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	281207	Squared	2.81207	High confidence	0.00001
		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	Low confidence	0.324024
	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	High confidence	5510.5
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	1.82499		19873	Low confidence	10889.4
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	High confidence	0.00001
	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	Low confidence	13
	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	High confidence	7523
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	Low confidence	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.