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

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Showing element 4736 to 4785 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2368	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Subtracted	162.86	163.712	0.852
2369	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]	Divided	218.555	219.434	1.00402
	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796]	Subtracted	212.724	213.574	0.85
2370	mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797]
	ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]	Divided	218.555	219.434	1.00402
2371	cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833]	Subtracted	212.724	213.574	0.85
	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]	Divided	218.555	219.434	1.00402
2372	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796]		212.724	213.574	1.004
	mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940]	Subtracted			0.85
2373	histone deacetylase 11 (hd11). [swissprot;acc:q96db2]
	mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797]	Divided			1.004
2374	cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833]
	ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9]	Subtracted			0.85
2375	ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6]
	mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940]	Divided			1.004
2376	hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232]	Subtracted			0.85
	histone deacetylase 11 (hd11). [swissprot;acc:q96db2]	Divided			1.004
2377	cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837]	Subtracted			0.85
	ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9]	Divided			1.004
2378	ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6]
	mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198]	Subtracted			0.85
2379	hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232]	Divided			1.004
	mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717]	Subtracted			0.85
2380	cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837]	Divided			1.004
	thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757]	Subtracted			0.85
2381	fibulin-1 precursor. [swissprot;acc:p23142]		192.348	191.503	0.845
	mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198]	Divided	212.724	213.574	1.004
2382	mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717]
	nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000]	Subtracted	213.82	212.983	0.837
2383	n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2]		221.662	220.826	0.836
	thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757]	Divided	212.724	213.574	1.004
2384	dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564]		210.57	209.737	1.00397
	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554]	Subtracted	198.181	197.346	0.835
2385	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
	dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734]	Divided	210.595	209.767	1.00395
2386	nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000]		213.82	212.983	1.00393
	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786]	Subtracted	214.966	215.799	0.833
2387	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960]
	proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074]	Divided	211.301	210.475	1.00392
2388	dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564]	Subtracted	210.57	209.737	0.833
	ring finger protein 20. [refseq;acc:nm_019592]	Divided	224.414	225.289	1.0039
2389	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127]	Subtracted	214.966	215.799	0.833
	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]	Divided	224.414	225.289	1.0039
2390	dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734]	Subtracted	210.595	209.767	0.828
	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786]	Divided	214.966	215.799	1.00388
2391	14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	Subtracted	220.683	221.51	0.827
	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960]	Divided	214.966	215.799	1.00388
2392	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127]
	proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074]	Subtracted	211.301	210.475	0.826
2393	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]		203.353	202.529	0.824

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.