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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Value Type  : Measured
Network Comparison Type  : Divided

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