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.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 19268 in total

Value Type  : Ranked
Filtered  : 0

green	Rank	Interaction Map	network_comparison	description	red	Network Comparison Type
0	501	High confidence	0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0	Subtracted
	502			brca1 associated protein. [refseq;acc:nm_006768]
	837	Low confidence		gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
	838			gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
	839			cobw-like protein. [refseq;acc:nm_018491]
	841			gamma-glutamyltransferase. [sptrembl;acc:q14390]
	842			gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
	843			gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
0.00001	501	High confidence	1	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001	Divided
	502			brca1 associated protein. [refseq;acc:nm_006768]
	837	Low confidence		gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
	838			gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
	839			cobw-like protein. [refseq;acc:nm_018491]
	841			gamma-glutamyltransferase. [sptrembl;acc:q14390]
	842			gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
	843			gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
394	500	High confidence	0	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	394	Subtracted
			1			Divided
	840	Low confidence	0			Subtracted
			1			Divided
696	209	High confidence	1.11351	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	775
	478		79			Subtracted
754	433		1.02387	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	772	Divided
	495		18			Subtracted
825	473		1.01103	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	816	Divided
	499		9			Subtracted
953	432		1.02473	fibrillin 3. [refseq;acc:nm_032447]	930	Divided
	492		23			Subtracted
1021	307		1.06856	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	1091	Divided
	483		70			Subtracted
1294	622	Low confidence	1.03025	caspr5 protein isoform 1. [refseq;acc:nm_130773]	1256	Divided
	623			contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]
	810		38	caspr5 protein isoform 1. [refseq;acc:nm_130773]		Subtracted
	812			contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]
1373	243	High confidence	1.09752	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	1251	Divided
	469		122			Subtracted
1521	466		1.01446	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	1543	Divided
	494		22			Subtracted
	730	Low confidence	1.01446			Divided
	820		22			Subtracted
1933	12		1.65028	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	3190	Divided
	195		1257			Subtracted
2582	21		1.49458	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	3859	Divided
	37	High confidence
	183		1277			Subtracted
	191	Low confidence
2668.83	832		1.00094	vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]	2671.33	Divided
	835		2.5			Subtracted
2695	76	High confidence	1.28905	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	3474	Divided
	290		779			Subtracted

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.