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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Value Type  : Measured
Network Comparison Type  : Divided

Rank	Filtered	description	Interaction Map	red	green	network_comparison
1	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	364	0.00001	36400000
			Low confidence
	1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		2399.5	543.5	4.4149
		rad50-interacting protein 1. [refseq;acc:nm_021930]	High confidence	450.5	2394.5	5.31521
2	0	cab2. [refseq;acc:nm_033419]		0.00001	174	17400000
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Low confidence		89	8900000
	1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		2399.5	543.5	4.4149
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	High confidence	450.5	2394.5	5.31521
3	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Low confidence	0.00001	89	8900000
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence		109	10900000
	1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Low confidence	2399.5	543.5	4.4149
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence	2597.5	698.5	3.71868
4	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	0.00001	89	8900000
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence
	1	hbs1-like. [refseq;acc:nm_006620]		2597.5	698.5	3.71868
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	2399.5	543.5	4.4149
5	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	High confidence	0.00001	89	8900000
		jumonji protein. [swissprot;acc:q92833]	Low confidence		17.5166	1751660
	1	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	High confidence	1153.5	339.5	3.39764
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence	736.5	2113.5	2.86965
6	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	High confidence	0.00001	89	8900000
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence	13	0.00001	1300000
	1	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	High confidence	1153.5	339.5	3.39764
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence	736.5	2113.5	2.86965
7	0	sedlin. [swissprot;acc:o14582]	High confidence	0.00001	43	4300000
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Low confidence	2.31962	0.00001	231962
	1	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]		736.5	2113.5	2.86965
		sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	High confidence	1153.5	339.5	3.39764
8	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Low confidence	85	6410	75.4118
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	High confidence	0.00001	43	4300000
	1	db83 protein. [swissprot;acc:p57088]		1153.5	339.5	3.39764
		phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Low confidence	3278	5058.5	1.54317
9	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	85	6410	75.4118
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence	383.762	10.6048	36.1876
	1	n33 protein. [swissprot;acc:q13454]		3278	5058.5	1.54317
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	High confidence	398.5	1281.5	3.21581
10	0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		85	6410	75.4118
		serpin b12. [swissprot;acc:q96p63]	Low confidence	199.549	5.56738	35.8425
	1	implantation-associated protein. [refseq;acc:nm_032121]		3278	5058.5	1.54317
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	High confidence	398.5	1281.5	3.21581
11	0	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Low confidence	199.249	5.71669	34.8539
		serpin b12. [swissprot;acc:q96p63]	High confidence	199.549	5.56738	35.8425
	1	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]		398.5	1281.5	3.21581
		thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	Low confidence	1917.64	2950.5	1.53861
12	0	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	High confidence	199.249	5.71669	34.8539
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Low confidence	859	58	14.8103
	1	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	High confidence	398.5	1281.5	3.21581
		gbp protein isoform a. [refseq;acc:nm_017870]	Low confidence	1921.96	2954.24	1.5371
13	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	High confidence	1363	47	29
		fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	Low confidence	8.11997	115.385	14.21

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.