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	Hugo	Network Comparison Type	Value Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 63874 to 63923 of 66312 in total

Interaction Map  : Low confidence
Filtered  : 1

Rank	description	Hugo	Network Comparison Type	Value Type	red	green	network_comparison
4757	iap-associated factor viaf1; phosducin-like 2. [refseq;acc:nm_024065]	PDCL3	Divided	Squared	44789.2	44224.2	1.01278
			Subtracted				565
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	MAGED2		Ranked	178.882	179.908	1.026
	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	MRPL3	Divided	Rooted	69.2175	70.391	1.01695
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	ITGB1BP3		Ranked	196.724	197.727	1.0051
	small membrane protein 1. [swissprot;acc:o95807]	TMEM50A		Measured	8550.04	8659.33	1.01278
	tripeptidyl-peptidase ii (ec 3.4.14.10) (tpp-ii) (tripeptidyl aminopeptidase). [swissprot;acc:p29144]	TPP2	Subtracted		8000.99	8104.75	103.76
4758	asparaginase-like 1 protein. [refseq;acc:nm_025080]	ASRGL1			7450.83	7554.21	103.38
	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	DCTD		Rooted	70.5678	71.7624	1.1946
	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	EXO1	Divided		75.6324	76.9139	1.01694
	proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070]	PSMB4		Ranked	200.524	199.513	1.00507
	putative dipeptidase. [refseq;acc:nm_022355]	DPEP2		Measured	8550.04	8659.33	1.01278
	trophinin. [swissprot;acc:q12816]	TRO	Subtracted	Ranked	178.882	179.908	1.026
	vigilin (high density lipoprotein-binding protein) (hdl-binding protein). [swissprot;acc:q00341]	HDLBP		Squared	47617.6	47057.3	560.3
	williams beuren syndrome chromosome region 21 isoform 1. [refseq;acc:nm_148912]	ABHD11	Divided		44789.3	44224.1	1.01278
4759	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	PDPK1	Subtracted	Ranked	206.842	205.83	1.012
	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	no value		Rooted	69.2568	70.4474	1.1906
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]			Measured	7511.52	7614.69	103.17
	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	DCTD	Divided	Rooted	70.5678	71.7624	1.01693
	membrane protein c21orf4. [swissprot;acc:p56557]	TMEM50B		Measured	8550.04	8659.33	1.01278
	monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	MGLL	Subtracted	Squared	46715.8	46159.1	556.7
	spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788]	SMS	Divided	Ranked	201.116	200.107	1.00504
	yippee-like protein 3 (digeorge syndrome-related protein fksg5). [swissprot;acc:q9bsj4]	YPEL3		Squared	49115.3	48495.6	1.01278
4760	atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288]	ABCD3		Rooted	70.668	71.8627	1.01691
	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]	AP2M1	Subtracted	Measured	7139.19	7242.17	102.98
	n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2]	NAT5	Divided	Squared	46533.2	45946.3	1.01277
	protein-l-isoaspartate(d-aspartate) o-methyltransferase (ec 2.1.1.77) (protein-beta-aspartate methyltransferase) (pimt) (protein l- isoaspartyl/d-aspartyl methyltransferase) (l-isoaspartyl protein carboxyl methyltransferase). [swissprot;acc:p22061]	PCMT1	Subtracted	Ranked	206.842	205.83	1.012
	putative metallopeptidase (family m19). [refseq;acc:nm_022357]	DPEP3	Divided	Measured	8550.04	8659.33	1.01278
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	RPL10L	Subtracted	Rooted	69.249	70.4371	1.1881
	wd-repeat protein 10. [swissprot;acc:q9hbg6]	IFT122	Divided	Ranked	204.904	203.878	1.00503
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	XAB1	Subtracted	Squared	47032.5	46477.1	555.4
4761	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	RPS14		Rooted	68.8727	70.0583	1.1856
	cyclin l1; cyclin l ania-6a. [refseq;acc:nm_020307]	CCNL1	Divided	Ranked	207.254	208.288	1.00499
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	MRPL4		Rooted	69.8301	71.0096	1.01689
	nuclear protein zap3 (zap113). [swissprot;acc:p49750]	YLPM1	Subtracted	Measured	8167.12	8270.02	102.9
	proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306]	CTRL	Divided		7877.1	7977.78	1.01278
	proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070]	PSMB4	Subtracted	Ranked	200.524	199.513	1.011
	ras-related protein rab-7. [swissprot;acc:p51149]	RAB7A		Squared	45104.1	44548.7	555.4
	vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106]	SCFD1	Divided		45915.2	45347.3	1.01252
4762	40s ribosomal protein s11. [swissprot;acc:p04643]	RPS11	Subtracted	Measured	7369.62	7472.14	102.52
	alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609]	ACTN2	Divided	Ranked	204.331	203.321	1.00497
			Subtracted				1.01
	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	CDK8	Divided	Rooted	70.3213	71.5004	1.01677
	elongation of very long chain fatty acids protein 4. [swissprot;acc:q9gzr5]	ELOVL4	Subtracted		70.3734	71.5529	1.1795
	homeobox protein msx-2 (hox-8). [swissprot;acc:p35548]	MSX2	Divided	Measured	8550.04	8659.33	1.01278
	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	GULP1	Subtracted	Squared	46111	45561.9	549.1
	ras-related protein rab-7. [swissprot;acc:p51149]	RAB7A	Divided		45104.1	44548.7	1.01247
4763	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	TRIP10			44782.1	44233	1.01241
			Subtracted				549.1
	cell matrix adhesion regulator (cell adhesion regulatory protein) (cell adhesion regulator). [swissprot;acc:q04762]	no value		Measured	7369.62	7472.14	102.52

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.