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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Gene	Filtered	Rank	description	Network Comparison Type	network_comparison	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	description	network_comparison	green	Value Type	Interaction Map	red
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	3.70633	15915	Ranked	High confidence	4294
	cab2. [refseq;acc:nm_033419]	716592	7.16592	Squared		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	0.00001	Rooted	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	14977	Ranked		5865
2	cab2. [refseq;acc:nm_033419]	17400000	174	Measured	High confidence	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	943398	9.43398	Rooted	Low confidence
		8900000	89	Measured
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	187479	1.87479	Squared
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	2.45711	21883	Ranked		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	0.00001	Squared		5.61325
		1240970		Rooted		12.4097
3	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	187479	1.87479	Squared	Low confidence	0.00001
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	943398	9.43398	Rooted
		8900000	89	Measured
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	2.14604	20617	Ranked		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	109	Measured		0.00001
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	561325	0.00001	Squared		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	0.823905	Squared	Low confidence	0.00001
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	943398	9.43398	Rooted
		8900000	89	Measured
	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	21883	Ranked		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	2.81207	Squared	High confidence	0.00001
		1044030	10.4403	Rooted
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	0.00001	Squared	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	7.68115	Rooted		0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	187479	1.87479	Squared	High confidence
		943398	9.43398	Rooted
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	8900000	89	Measured
	jumonji protein. [swissprot;acc:q92833]	1751660	17.5166		Low confidence
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	2.17144	11965.7	Ranked	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	0.00001	Rooted		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	89	Measured	High confidence	0.00001
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	187479	1.87479	Squared
		943398	9.43398	Rooted
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	1300000	0.00001	Measured	Low confidence	13
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	1.71877	9583.37	Ranked		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	0.00001	Rooted	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.