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.

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

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Showing element 3030 to 3079 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

red	Rank	description	green	network_comparison
9921.43	874	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	10941.2	1.10278
9946.21	1931	ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1]	9367.66	1.06176
10067.9	504	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	11511	1.14334
10075.5	1500	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	9377.75	1.0744
	1501	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
	1502	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
	1503	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
	1504	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
	1505	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
10143.6	2744	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	10163.6	1.00197
10178.5	2070	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	9638.08	1.05607
10198.1	2742	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	10174.3	1.00234
10230.1	905	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	11256.2	1.1003
10231.8	1370	t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	9487.34	1.07847
	1371	double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]
10235.2	420	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	11830.8	1.15589
10241.3	2029	paraspeckle protein 1. [refseq;acc:nm_018282]	9685.21	1.05742
10243.4	2028	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233]	9686.82	1.05746
10246.1	902	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	11285.8	1.10147
10247.8	895	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	11289	1.1016
10263.8	875	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	11318.6	1.10277
10264.9	567	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316]	9043.51	1.13506
10300	1932	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	9701.33	1.06171
	1933	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]
10341.2	1518	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]	9630.35	1.07381
10430.3	1335	coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618]	9656.4	1.08014
10434.4	565	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	11846.2	1.1353
10599.9	543	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	12064.7	1.13819
10600.3	541	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	12065.2
10603.5	535	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	12069.5	1.13826
	536	calsyntenin-1 precursor. [swissprot;acc:o94985]
	537	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]
	538	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	12069.4	1.13825
	539	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]
	540	gk001 protein. [refseq;acc:nm_020198]
10635.3	528	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	12111.4	1.13879
10639.8	525	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	12117.3	1.13887
10639.9	526	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	12117.4	1.13886
10640	524	aquaporin 5. [swissprot;acc:p55064]	12117.6	1.13887
10640.2	523	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	12117.8
10719	1256	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	9891.08	1.0837
10725.6	1254	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	9896.32	1.0838
10733.4	1250	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	9902.6	1.0839
10804.7	495	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	12363.6	1.14428
10807.4	512	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	12338.5	1.14167
10872.4	488	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	12447	1.14483
10908.6	486	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	12491.8	1.14513
11004.2	356	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	12944.2	1.1763
11068	146	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	8508.5	1.30082
	147	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]

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.