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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Network Comparison Type  : Divided
Value Type  : Measured

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

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.