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

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Showing element 1 to 50 of 77072 in total

Network Comparison Type  : Divided
Value Type  : Measured

Rank	Interaction Map	green	network_comparison	description	red	Filtered
1	High confidence	0.00001	36400000	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0
		2394.5	5.31521	rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	1
	Low confidence	0.00001	36400000	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0
		543.5	4.4149	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	2399.5	1
2	High confidence	174	17400000	cab2. [refseq;acc:nm_033419]	0.00001	0
		2394.5	5.31521	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	1
	Low confidence	89	8900000	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	0
		543.5	4.4149	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	2399.5	1
3	High confidence	109	10900000	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001	0
		698.5	3.71868	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	1
	Low confidence	89	8900000	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	0
		543.5	4.4149	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	2399.5	1
4	High confidence	89	8900000	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	0
		698.5	3.71868	hbs1-like. [refseq;acc:nm_006620]	2597.5	1
	Low confidence	89	8900000	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0.00001	0
		543.5	4.4149	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	2399.5	1
5	High confidence	89	8900000	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	0
		339.5	3.39764	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1153.5	1
	Low confidence	17.5166	1751660	jumonji protein. [swissprot;acc:q92833]	0.00001	0
		2113.5	2.86965	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	736.5	1
6	High confidence	89	8900000	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0.00001	0
		339.5	3.39764	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1153.5	1
	Low confidence	0.00001	1300000	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	13	0
		2113.5	2.86965	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	736.5	1
7	High confidence	43	4300000	sedlin. [swissprot;acc:o14582]	0.00001	0
		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
	Low confidence	0.00001	231962	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	2.31962	0
		2113.5	2.86965	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	736.5	1
8	High confidence	43	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
	Low confidence	5058.5	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	High confidence	1281.5	3.21581	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	398.5	1
		6410	75.4118	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	0
	Low confidence	10.6048	36.1876	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	383.762
		5058.5	1.54317	n33 protein. [swissprot;acc:q13454]	3278	1
10	High confidence	1281.5	3.21581	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5
		6410	75.4118	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	0
	Low confidence	5.56738	35.8425	serpin b12. [swissprot;acc:q96p63]	199.549
		5058.5	1.54317	implantation-associated protein. [refseq;acc:nm_032121]	3278	1
11	High confidence	5.56738	35.8425	serpin b12. [swissprot;acc:q96p63]	199.549	0
		1281.5	3.21581	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	398.5	1
	Low confidence	5.71669	34.8539	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	0
		2950.5	1.53861	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	1917.64	1
12	High confidence	5.71669	34.8539	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	0
		1281.5	3.21581	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	398.5	1
	Low confidence	58	14.8103	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	0
		2954.24	1.5371	gbp protein isoform a. [refseq;acc:nm_017870]	1921.96	1
13	High confidence	47	29	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	1363	0
		1281.5	3.21581	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	1

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.