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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 9634 in total

Value Type  : Measured
Network Comparison Type  : Divided

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