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	Interaction Map	green	Network Comparison Type	red	network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

Rank	description	Value Type	Interaction Map	green	red	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	High confidence	15915	4294	3.70633
	cab2. [refseq;acc:nm_033419]	Squared		7.16592	0.00001	716592
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Low confidence	1.87479		187479
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	High confidence	0.00001	364	36400000
			Low confidence
		Rooted	High confidence		19.0788	1907880
			Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked		14977	5865	2.55362
2	cab2. [refseq;acc:nm_033419]	Measured	High confidence	174	0.00001	17400000
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Low confidence	89		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	8906	2.45711
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		High confidence	14977	5865	2.55362
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared		0.00001	5.61325	561325
		Rooted			12.4097	1240970
3	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	Low confidence	1.87479	0.00001	187479
	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	9607	2.14604
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		High confidence	11083.9	4475.84	2.47638
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured		109	0.00001	10900000
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared		0.00001	5.61325	561325
		Rooted			12.4097	1240970
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	Low confidence	0.823905	0.00001	82390.5
	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	High confidence	89		8900000
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked		21883	8906	2.45711
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]		Low confidence	20617	9607	2.14604
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared	High confidence	2.81207	0.00001	281207
		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	Low confidence	0.00001	0.324024	32402.4
	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]	Rooted		7.68115	0.00001	768115
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	High confidence	1.87479		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]		Low confidence	17.5166		1751660
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Ranked	High confidence	11965.7	5510.5	2.17144
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]		Low confidence	19873	10889.4	1.82499
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	6.08276	608276
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Squared			0.324024	32402.4
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	High confidence	89	0.00001	8900000
	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	Low confidence	0.00001	13	1300000
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Ranked		9583.37	5575.71	1.71877
	ubiquitin protein ligase. [refseq;acc:nm_130466]		High confidence	15339.2	7523	2.03897
7	cab2. [refseq;acc:nm_033419]			10950	21866	1.99689
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Rooted	Low confidence	0.00001	6.08276	608276

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.