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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1958 to 2007 of 6456 in total

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

Rank	description	Hugo	Network Comparison Type	red	green	network_comparison
979	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]	PRKCI	Subtracted	211.987	204.964	7.023
980	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	BRAF	Divided	130.289	134.713	1.03396
	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	NUMB	Subtracted	211.987	204.964	7.023
981	exocyst complex component sec6. [swissprot;acc:o60645]	EXOC3	Divided	207.186	200.398	1.03387
	tbc1 domain family member 5. [swissprot;acc:q92609]	TBC1D5	Subtracted	211.987	204.964	7.023
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	CIRH1A	Divided	243.312	235.351	1.03383
	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	TULP1	Subtracted	211.987	204.964	7.023
983	pbk1 protein. [sptrembl;acc:o76021]	RSL1D1	Divided	243.312	235.353	1.03382
	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]	VPS29	Subtracted	211.987	204.964	7.023
984	numb-like protein (numb-r). [swissprot;acc:q9y6r0]	NUMBL
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	PAPOLA	Divided	116.71	120.654	1.03379
985	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	PDCD5		233.402	225.782	1.03375
	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]	TULP3	Subtracted	211.987	204.964	7.023
986	exocyst complex component sec5. [swissprot;acc:q96kp1]	EXOC2	Divided	116.771	120.707	1.03371
	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]	VPS35	Subtracted	211.987	204.964	7.023
987	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]	PRKCZ
	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	HTRA2	Divided	218.459	211.338	1.03369
988	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	HTRA4		218.461	211.343	1.03368
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	no value	Subtracted	236.679	243.679	7
989	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	HTRA3	Divided	218.462	211.345	1.03367
	zinc finger protein 277. [swissprot;acc:q9nrm2]	no value	Subtracted	236.679	243.679	7
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	DDX52	Divided	243.297	235.373	1.03367
	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	MAGI2	Subtracted	221.682	228.68	6.998
991	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	DPM1	Divided	203.381	196.76	1.03365
	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	EXOSC10	Subtracted	198.494	205.466	6.972
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	HTRA1	Divided	218.468	211.357	1.03364
	vinculin (metavinculin). [swissprot;acc:p18206]	VCL	Subtracted	215.92	208.95	6.97
993	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541]	HNF4G		251.863	258.829	6.966
	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	PNN	Divided	211.071	204.205	1.03362
994	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]	GADD45G	Subtracted	251.863	258.829	6.966
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	PAPOLG	Divided	116.845	120.772	1.03361
995	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]	GADD45A	Subtracted	251.863	258.829	6.966
	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	MAD2L2	Divided	219.656	212.547	1.03345
996	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]	HNF4A	Subtracted	251.863	258.829	6.966
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	no value	Divided	219.656	212.547	1.03345
997	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]	GADD45B	Subtracted	251.863	258.829	6.966
	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]	NUP88	Divided	219.656	212.547	1.03345
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	DYNC1I2		225.557	218.271	1.03338
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	TYRL	Subtracted	221.302	214.409	6.893
999	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	FHL2		269.608	276.493	6.885
	vinculin (metavinculin). [swissprot;acc:p18206]	VCL	Divided	215.92	208.95	1.03336
1000	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	CROT	Subtracted	217.523	210.648	6.875
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	no value	Divided	225.167	217.922	1.03325
1001	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	DCT	Subtracted	221.28	214.409	6.871
	sprouty homolog 3 (spry-3). [swissprot;acc:o43610]	SPRY3	Divided	225.167	217.922	1.03325
1002	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	TYRP1	Subtracted	221.278	214.409	6.869
	sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]	SPRY1	Divided	225.167	217.922	1.03325
1003	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	PNN	Subtracted	211.071	204.205	6.866
	sprouty homolog 2 (spry-2). [swissprot;acc:o43597]	SPRY2	Divided	225.167	217.922	1.03325
1004	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	no value		238.725	231.059	1.03318

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.