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

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Showing element 1 to 50 of 38536 in total

Value Type  : Measured
Network Comparison Type  : Divided

Rank	Interaction Map	Filtered	description	network_comparison	green	red
1	High confidence	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	0.00001	364
		1	rad50-interacting protein 1. [refseq;acc:nm_021930]	5.31521	2394.5	450.5
	Low confidence	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	0.00001	364
		1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	4.4149	543.5	2399.5
2	High confidence	0	cab2. [refseq;acc:nm_033419]	17400000	174	0.00001
		1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	5.31521	2394.5	450.5
	Low confidence	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	8900000	89	0.00001
		1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	4.4149	543.5	2399.5
3	High confidence	0	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	10900000	109	0.00001
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	3.71868	698.5	2597.5
	Low confidence	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	8900000	89	0.00001
		1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	4.4149	543.5	2399.5
4	High confidence	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	8900000	89	0.00001
		1	hbs1-like. [refseq;acc:nm_006620]	3.71868	698.5	2597.5
	Low confidence	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	8900000	89	0.00001
		1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	4.4149	543.5	2399.5
5	High confidence	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	8900000	89	0.00001
		1	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	3.39764	339.5	1153.5
	Low confidence	0	jumonji protein. [swissprot;acc:q92833]	1751660	17.5166	0.00001
		1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	2.86965	2113.5	736.5
6	High confidence	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	8900000	89	0.00001
		1	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	3.39764	339.5	1153.5
	Low confidence	0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	1300000	0.00001	13
		1	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	2.86965	2113.5	736.5
7	High confidence	0	sedlin. [swissprot;acc:o14582]	4300000	43	0.00001
		1	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]	3.39764	339.5	1153.5
	Low confidence	0	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	231962	0.00001	2.31962
		1	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	2.86965	2113.5	736.5
8	High confidence	0	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	4300000	43	0.00001
		1	db83 protein. [swissprot;acc:p57088]	3.39764	339.5	1153.5
	Low confidence	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	75.4118	6410	85
		1	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	1.54317	5058.5	3278
9	High confidence	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	75.4118	6410	85
		1	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	3.21581	1281.5	398.5
	Low confidence	0	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	36.1876	10.6048	383.762
		1	n33 protein. [swissprot;acc:q13454]	1.54317	5058.5	3278
10	High confidence	0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	75.4118	6410	85
		1	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	3.21581	1281.5	398.5
	Low confidence	0	serpin b12. [swissprot;acc:q96p63]	35.8425	5.56738	199.549
		1	implantation-associated protein. [refseq;acc:nm_032121]	1.54317	5058.5	3278
11	High confidence	0	serpin b12. [swissprot;acc:q96p63]	35.8425	5.56738	199.549
		1	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	3.21581	1281.5	398.5
	Low confidence	0	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	5.71669	199.249
		1	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	1.53861	2950.5	1917.64
12	High confidence	0	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	5.71669	199.249
		1	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	3.21581	1281.5	398.5
	Low confidence	0	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14.8103	58	859
		1	gbp protein isoform a. [refseq;acc:nm_017870]	1.5371	2954.24	1921.96
13	High confidence	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	29	47	1363
		1	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	3.21581	1281.5	398.5

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.