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

Results: HTML CSV LaTeX

Showing element 3008 to 3057 of 16578 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1

Rank	description	Hugo	Interaction Map	red	green	network_comparison
1504	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307]	CDC25C	High confidence	259.439	254.797	1.01822
1505	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897]	QARS	Low confidence	202.722	198.48	1.02137
	protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0]	CCDC53	High confidence	216.158	212.316	1.0181
1506	c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0]	C16orf42		212.103	208.339	1.01807
	ras-related protein rab-8b. [swissprot;acc:q92930]	RAB8B	Low confidence	200.685	196.487	1.02137
1507	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281]	ATP6V1B2		198.931	194.769
	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118]	PDK1	High confidence	213.274	209.5	1.01801
1508	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	CTH	Low confidence	203.663	199.402	1.02137
	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119]	PDK2	High confidence	213.274	209.5	1.01801
1509	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024]	ACTR1A		225.148	221.177	1.01795
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	no value	Low confidence	204.422	200.147	1.02136
1510	beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025]	ACTR1B	High confidence	225.148	221.177	1.01795
	peroxiredoxin 1 (ec 1.11.1.-) (thioredoxin peroxidase 2) (thioredoxin- dependent peroxide reductase 2) (proliferation-associated protein pag) (natural killer cell enhancing factor a) (nkef-a). [swissprot;acc:q06830]	PRDX1	Low confidence	200.965	196.762	1.02136
1511	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1]	COX11	High confidence	213.268	209.509	1.01794
	long-chain-fatty-acid--coa ligase 2 (ec 6.2.1.3) (long-chain acyl-coa synthetase 2) (lacs 2). [swissprot;acc:p33121]	ACSL1	Low confidence	204.294	200.024	1.02135
1512	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162]	PRDX4		201.123	196.918
	surfeit locus protein 1. [swissprot;acc:q15526]	SURF1	High confidence	213.268	209.509	1.01794
1513	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]	COX15
	peroxiredoxin 2 (ec 1.11.1.-) (thioredoxin peroxidase 1) (thioredoxin- dependent peroxide reductase 1) (thiol-specific antioxidant protein) (tsa) (prp) (natural killer cell enhancing factor b) (nkef-b). [swissprot;acc:p32119]	PRDX2	Low confidence	200.934	196.735	1.02134
1514	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]	GPT2		195.292	191.212
	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]	COX10	High confidence	213.268	209.509	1.01794
1515	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868]	DPP10		213.267	209.511	1.01793
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	no value	Low confidence	202.972	198.731	1.02134
1516	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	DPP6	High confidence	213.267	209.511	1.01793
	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313]	ATP6V1B1	Low confidence	198.978	194.82	1.02134
1517	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884]	FAP	High confidence	213.267	209.511	1.01793
	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]	SARS2	Low confidence	193.118	189.083	1.02134
1518	dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695]	APEX1		200.093	195.912
	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874]	BCKDK	High confidence	213.259	209.524	1.01783
1519	cone-rod homeobox protein. [swissprot;acc:o43186]	CRX		244.331	240.061	1.01779
	long-chain-fatty-acid--coa ligase 5 (ec 6.2.1.3) (long-chain acyl-coa synthetase 5) (lacs 5). [swissprot;acc:q9ulc5]	no value	Low confidence	204.295	200.027	1.02134
1520	homeobox protein otx1. [swissprot;acc:p32242]	OTX1	High confidence	244.367	240.098	1.01778
	ras-related protein rab-8 (rab-8a) (oncogene c-mel). [swissprot;acc:p24407]	RAB8A	Low confidence	200.683	196.493	1.02132
1521	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	ARMET		203.641	199.39
	homeobox protein otx2. [swissprot;acc:p32243]	OTX2	High confidence	244.478	240.212	1.01776
1522	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	CIRH1A	Low confidence	203.989	199.731	1.02132
	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949]	MPI	High confidence	219.306	223.179	1.01766
1523	putative ankyrin-repeat containing protein. [refseq;acc:nm_025185]	no value
	transcription factor bteb1 (basic transcription element binding protein 1) (bte-binding protein 1) (gc box binding protein 1) (krueppel-like factor 9). [swissprot;acc:q13886]	KLF9	Low confidence	204.205	199.943	1.02132
1524	autoantigen. [refseq;acc:nm_014329]	EDC4		204.696	200.423
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	STARD3	High confidence	219.306	223.179	1.01766
1525	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8]	FAT2
	transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072]	VCP	Low confidence	202.419	198.197	1.0213
1526	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]	FAT	High confidence	219.306	223.179	1.01766
	krueppel-like factor 13 (transcription factor bteb3) (basic transcription element binding protein 3) (bte-binding protein 3) (rantes factor of late activated t lymphocytes-1) (rflat-1) (transcription factor nslp1) (novel sp1-like zinc finger transcription factor 1). [swissprot;acc:q9y2y9]	KLF13	Low confidence	204.198	199.941	1.02129
1527	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]	STARD3NL	High confidence	219.306	223.179	1.01766
	transcription factor sp2. [swissprot;acc:q02086]	SP2	Low confidence	204.196	199.94	1.02129
1528	cgi-121 protein; prpk (p53-related protein kinase)-binding protein. [refseq;acc:nm_016058]	TPRKB		192.391	188.381
	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318]	FOXA3	High confidence	217.785	214.021	1.01759
1529	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	ACTG1		216.762	213.031	1.01751

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
- Hugo is the HGNC identifier if it exists
- 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.