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 [...,...].

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

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

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.