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