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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 4558 to 4607 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
2279	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275]	Divided	190.909	191.936	1.00538
2280	epsin 3. [refseq;acc:nm_017957]	Subtracted	219.284	218.153	1.131
	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818]	Divided	211.657	212.793	1.00537
2281	splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333]		218.482	219.652	1.00536
	tripartite motif protein 2. [swissprot;acc:q9c040]	Subtracted	203.437	202.312	1.125
2282	dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887]		208.44	207.319	1.121
	splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081]	Divided	218.482	219.652	1.00536
2283	proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3]		211.676	212.81
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Subtracted	234.905	236.023	1.118
2284	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]		162.665	161.547
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Divided	218.482	219.652	1.00536
2285	nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177]	Subtracted	218.498	217.392	1.106
	splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368]	Divided	218.482	219.652	1.00536
2286	delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886]	Subtracted	218.498	217.392	1.106
	dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518]	Divided	215.456	216.608	1.00535
2287	phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393]		205.376	206.475
	ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068]	Subtracted	216.339	215.239	1.1
2288	dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740]	Divided	215.458	216.607	1.00533
	udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701]	Subtracted	216.339	215.239	1.1
2289	dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512]	Divided	215.46	216.605	1.00531
	phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393]	Subtracted	205.376	206.475	1.099
2290	myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368]	Divided	201.213	200.158	1.00527
	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	Subtracted	179.999	181.091	1.092
2291	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Divided	201.213	200.158	1.00527
	ubiquitin. [swissprot;acc:p02248]	Subtracted	215.529	216.617	1.088
2292	camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861]		214.467	215.554	1.087
	ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441]	Divided	201.213	200.158	1.00527
2293	large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379]
	protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817]	Subtracted	214.459	215.543	1.084
2294	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]			215.542	1.083
	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Divided	163.187	162.331	1.00527
2295	camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694]	Subtracted	214.459	215.542	1.083
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Divided	163.712	162.86	1.00523
2296	camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612]	Subtracted	214.459	215.542	1.083
	phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939]	Divided	205.38	206.451	1.00521
2297	camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323]	Subtracted	214.449	215.529	1.08
	epsin 3. [refseq;acc:nm_017957]	Divided	219.284	218.153	1.00518
2298	rad54-like protein; rad54 homolog. [refseq;acc:nm_003579]	Subtracted	218.218	219.292	1.074
	ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068]	Divided	216.339	215.239	1.00511
2299	phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939]	Subtracted	205.38	206.451	1.071
	udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701]	Divided	216.339	215.239	1.00511
2300	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	Subtracted	218.311	217.241	1.07
	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	Divided	192.541	191.563	1.00511
2301	nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177]		218.498	217.392	1.00509
	symplekin. [swissprot;acc:q92797]	Subtracted	163.8	162.741	1.059
2302	hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868]	Divided	192.542	191.567	1.00509
	myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368]	Subtracted	201.213	200.158	1.055
2303	3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]	Divided	192.542	191.567	1.00509
	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Subtracted	201.213	200.158	1.055
2304	hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581]	Divided	192.542	191.567	1.00509

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.