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	network_comparison	green	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	network_comparison	green	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	1	0.00001	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	1.02387	754	High confidence	trinucleotide repeat containing 15. [refseq;acc:nm_015575]
	Subtracted	495	18
775	Divided	209	1.11351	696		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]
	Subtracted	478	79
816	Divided	473	1.01103	825		cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]
	Subtracted	499	9
930	Divided	432	1.02473	953		fibrillin 3. [refseq;acc:nm_032447]
	Subtracted	492	23
1091	Divided	307	1.06856	1021		ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]
	Subtracted	483	70
1251	Divided	243	1.09752	1373		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	1.03025	1294	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	1.01446	1521	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	1.07276	2772		hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433]
	Subtracted	704	188
2671.33	Divided	832	1.00094	2668.83		vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]
	Subtracted	835	2.5
2939	Divided	448	1.02191	2876	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	1.03595	3141		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.