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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 3730 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	green	network_comparison
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	364	0.00001	36400000
	rad50-interacting protein 1. [refseq;acc:nm_021930]	1	450.5	2394.5	5.31521
2	cab2. [refseq;acc:nm_033419]	0	0.00001	174	17400000
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	450.5	2394.5	5.31521
3	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		2597.5	698.5	3.71868
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	0.00001	109	10900000
4	hbs1-like. [refseq;acc:nm_006620]	1	2597.5	698.5	3.71868
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	0.00001	89	8900000
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1	1153.5	339.5	3.39764
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	0.00001	89	8900000
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1	1153.5	339.5	3.39764
7	sedlin. [swissprot;acc:o14582]	0	0.00001	43	4300000
	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]	1	1153.5	339.5	3.39764
8	db83 protein. [swissprot;acc:p57088]
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	0.00001	43	4300000
9	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		85	6410	75.4118
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	398.5	1281.5	3.21581
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	85	6410	75.4118
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1	398.5	1281.5	3.21581
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
	serpin b12. [swissprot;acc:q96p63]	0	199.549	5.56738	35.8425
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	1	398.5	1281.5	3.21581
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	0	199.249	5.71669	34.8539
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		1363	47	29
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	1	398.5	1281.5	3.21581
14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	0	130.512	6.50325	20.0687
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1	398.5	1281.5	3.21581
15	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	0	10	156	15.6
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	2671	871	3.06659
16	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0	1	15	15
	protein x 0004. [refseq;acc:nm_016301]	1	2671	871	3.06659
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		460	1365	2.96739
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	859	58	14.8103
18	60s ribosomal protein l37a. [swissprot;acc:p12751]		305.45	26.1599	11.6763
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	677.5	1865.5	2.75351
19	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	0	305.45	26.1599	11.6763
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	677.5	1865.5	2.75351
20	ero1-like. [refseq;acc:nm_014584]	0	82	0.00001	8200000
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	1	677.5	1865.5	2.75351
21	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
	syntaxin 10 (syn10). [swissprot;acc:o60499]	0	118.878	17.6611	6.73106
22	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	1	677.5	1865.5	2.75351
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	60	0.00001	6000000
23	gbp protein isoform a. [refseq;acc:nm_017870]	1	699.76	1894.39	2.7072
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0	0.00001	59	5900000
24	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	950.561	2108.52	2.21818
	ptd016 protein. [refseq;acc:nm_016125]	0	30	158	5.26667
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1	1833.01	892.67	2.0534
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	0	148	773	5.22297

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.