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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 19268 in total

Filtered  : 0
Value Type  : Ranked

red	Network Comparison Type	Rank	green	network_comparison	Interaction Map	description
0	Subtracted	501	0	0	High confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		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	Divided	501	0.00001	1	High confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		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	394		High confidence	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]
		840			Low confidence
	Subtracted	500		0	High confidence
		840			Low confidence
772	Divided	433	754	1.02387	High confidence	trinucleotide repeat containing 15. [refseq;acc:nm_015575]
	Subtracted	495		18
775	Divided	209	696	1.11351		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]
	Subtracted	478		79
816	Divided	473	825	1.01103		cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]
	Subtracted	499		9
930	Divided	432	953	1.02473		fibrillin 3. [refseq;acc:nm_032447]
	Subtracted	492		23
1091	Divided	307	1021	1.06856		ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]
	Subtracted	483		70
1251	Divided	243	1373	1.09752		polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]
	Subtracted	469		122
1256	Divided	622	1294	1.03025	Low confidence	caspr5 protein isoform 1. [refseq;acc:nm_130773]
		623				contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]
	Subtracted	810		38		caspr5 protein isoform 1. [refseq;acc:nm_130773]
		812				contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]
1543	Divided	466	1521	1.01446	High confidence	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
		730			Low confidence
	Subtracted	494		22	High confidence
		820			Low confidence
2584	Divided	450	2772	1.07276		hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433]
	Subtracted	704		188
2671.33	Divided	832	2668.83	1.00094		vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]
	Subtracted	835		2.5
2939	Divided	448	2876	1.02191	High confidence	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]
		674			Low confidence
	Subtracted	484		63	High confidence
		796			Low confidence
3032	Divided	602	3141	1.03595		erythropoietin 4 immediate early response; uncharacterized hypothalamus protein ht010. [refseq;acc:nm_018471]
	Subtracted	757		109

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.