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	Rank	Gene	Interaction Map	green	description	red	network_comparison	Filtered

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Network Comparison Type  : Divided
Value Type  : Measured

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