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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

Rank	description	Value Type	green	Interaction Map	network_comparison	red
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	15915	High confidence	3.70633	4294
	cab2. [refseq;acc:nm_033419]	Squared	7.16592		716592	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		1.87479	Low confidence	187479
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	0.00001	High confidence	36400000	364
				Low confidence
		Rooted		High confidence	1907880	19.0788
				Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked	14977		2.55362	5865
2	cab2. [refseq;acc:nm_033419]	Measured	174	High confidence	17400000	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89	Low confidence	8900000
		Rooted	9.43398		943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared	1.87479		187479
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked	21883		2.45711	8906
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		14977	High confidence	2.55362	5865
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	0.00001		561325	5.61325
		Rooted			1240970	12.4097
3	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	1.87479	Low confidence	187479	0.00001
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured	89		8900000
		Rooted	9.43398		943398
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Ranked	20617		2.14604	9607
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		11083.9	High confidence	2.47638	4475.84
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured	109		10900000	0.00001
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared	0.00001		561325	5.61325
		Rooted			1240970	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]	Squared	0.823905	Low confidence	82390.5	0.00001
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	89		8900000
		Rooted	9.43398		943398
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	89	High confidence	8900000
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked	21883		2.45711	8906
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]		20617	Low confidence	2.14604	9607
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared	2.81207	High confidence	281207	0.00001
		Rooted	10.4403		1044030
5	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Squared	0.00001	Low confidence	32402.4	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]	Rooted	7.68115		768115	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	1.87479	High confidence	187479
		Rooted	9.43398		943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured	89		8900000
	jumonji protein. [swissprot;acc:q92833]		17.5166	Low confidence	1751660
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Ranked	11965.7	High confidence	2.17144	5510.5
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]		19873	Low confidence	1.82499	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]	Rooted	0.00001		608276	6.08276
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Squared			32402.4	0.324024
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	89	High confidence	8900000	0.00001
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared	1.87479		187479
		Rooted	9.43398		943398
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Measured	0.00001	Low confidence	1300000	13
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Ranked	9583.37		1.71877	5575.71
	ubiquitin protein ligase. [refseq;acc:nm_130466]		15339.2	High confidence	2.03897	7523
7	cab2. [refseq;acc:nm_033419]		10950		1.99689	21866
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Rooted	0.00001	Low confidence	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.