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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Filtered	Gene	Rank	Network Comparison Type	description	Interaction Map	green	Value 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	Interaction Map	green	Value Type	red	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	High confidence	15915	Ranked	4294	3.70633
	cab2. [refseq;acc:nm_033419]		7.16592	Squared	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]	High confidence	0.00001	Measured	364	36400000
				Rooted	19.0788	1907880
		Low confidence		Measured	364	36400000
				Rooted	19.0788	1907880
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		14977	Ranked	5865	2.55362
2	cab2. [refseq;acc:nm_033419]	High confidence	174	Measured	0.00001	17400000
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Low confidence	9.43398	Rooted		943398
			89	Measured		8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		1.87479	Squared		187479
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		21883	Ranked	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]		0.00001	Squared	5.61325	561325
				Rooted	12.4097	1240970
3	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	1.87479	Squared	0.00001	187479
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		9.43398	Rooted		943398
			89	Measured		8900000
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]		20617	Ranked	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]		109	Measured	0.00001	10900000
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		0.00001	Squared	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]	Low confidence	0.823905	Squared	0.00001	82390.5
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		9.43398	Rooted		943398
			89	Measured		8900000
	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]		21883	Ranked	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]	High confidence	2.81207	Squared	0.00001	281207
			10.4403	Rooted		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]	Low confidence	0.00001	Squared	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]		7.68115	Rooted	0.00001	768115
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence	1.87479	Squared		187479
			9.43398	Rooted		943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		89	Measured		8900000
	jumonji protein. [swissprot;acc:q92833]	Low confidence	17.5166			1751660
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	High confidence	11965.7	Ranked	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]		0.00001	Rooted	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]	High confidence	89	Measured	0.00001	8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		1.87479	Squared		187479
			9.43398	Rooted		943398
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence	0.00001	Measured	13	1300000
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]		9583.37	Ranked	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]	Low confidence	0.00001	Rooted	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.