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 57674 to 57723 of 66312 in total

Interaction Map  : Low confidence
Filtered  : 1

Rank	description	Hugo	Value Type	Network Comparison Type	red	green	network_comparison
3982	g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849]	GRSF1	Squared	Subtracted	43640.6	42422.7	1217.9
	heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792]	HSPB1	Ranked		205.901	203.522	2.379
	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	NME3	Squared	Divided	45834.1	44570.5	1.02835
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	RPS27L	Ranked		203.038	200.645	1.01193
	sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9]	SALL3	Rooted		70.7779	72.7204	1.02745
	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	SQSTM1	Measured		8221.64	8406.32	1.02246
	zinc finger-like protein (fragment). [sptrembl;acc:q9uia8]	ZNF497		Subtracted	9143.31	9323.17	179.86
3983	alpha 2 globin. [refseq;acc:nm_000517]	no value	Squared		42064.6	40846.7	1217.9
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]		Rooted	Divided	70.9824	72.9304	1.02744
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	MLH1	Ranked	Subtracted	201.031	198.658	2.373
	proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789]	PSMA4	Rooted		71.9597	73.9293	1.9696
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	CHMP4A	Squared	Divided	41987.1	40829.5	1.02835
	tbp-associated factor 1b; tata box binding protein (tbp)-associated factor, rna polymerase i, b, 63kd; sl1, 63kd subunit. [refseq;acc:nm_005680]	TAF1B	Measured		8124.9	8307.41	1.02246
	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	TRIO	Ranked		203.287	200.891	1.01193
	zinc finger protein 350; zinc-finger protein zbrk1. [refseq;acc:nm_021632]	ZNF350	Measured	Subtracted	9143.33	9323.19	179.86
3984	atp-dependent dna helicase q1 (dna-dependent atpase q1). [swissprot;acc:p46063]	RECQL	Squared	Divided	46495	45213.5	1.02834
	cell division cycle 2-like protein kinase 5 (ec 2.7.1.-) (cholinesterase-related cell division controller) (cdc2-related protein kinase 5). [swissprot;acc:q14004]	CDC2L5	Ranked		202.774	200.388	1.01191
	dachshund homolog isoform a. [refseq;acc:nm_080759]	DACH1		Subtracted	202.446	200.075	2.371
	heat-shock protein 105 kda (heat shock 110 kda protein) (antigen ny-co-25). [swissprot;acc:q92598]	HSPH1	Rooted	Divided	71.4034	73.3624	1.02744
	hemoglobin theta-1 chain. [swissprot;acc:p09105]	HBQ1	Squared	Subtracted	42064.6	40846.7	1217.9
	laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	LAMB1	Measured	Divided	7915.74	8093.54	1.02246
	tata element modulatory factor (tmf). [swissprot;acc:p82094]	TMF1	Rooted	Subtracted	75.6341	77.6028	1.9687
	zinc finger protein 398 (zinc finger dna binding protein p52/p71). [swissprot;acc:q8td17]	ZNF282	Measured		9143.32	9323.18	179.86
3985	acyl-coenzyme a oxidase 3, peroxisomal (ec 1.3.3.6) (pristanoyl-coa oxidase). [swissprot;acc:o15254]	ACOX3		Divided	8124.9	8307.41	1.02246
	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]	FTL	Rooted		70.9824	72.9302	1.02744
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	NUDT12		Subtracted	71.3167	73.2852	1.9685
	p120e4f. [refseq;acc:nm_004424]	E4F1	Measured		9143.32	9323.18	179.86
	potential phospholipid-transporting atpase ia (ec 3.6.3.1) (chromaffin granule atpase ii) (atpase class i type 8a member 1). [swissprot;acc:q9y2q0]	ATP8A1	Squared	Divided	45949.8	44683.8	1.02833
	protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6]	PACSIN3	Ranked		201.469	199.1	1.0119
	set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105]	SET		Subtracted	202.446	200.075	2.371
	tumor protein d52 (n8 protein). [swissprot;acc:p55327]	TPD52	Squared		46258.5	45041	1217.5
3986	2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664]	DECR2	Rooted		72.7042	74.6723	1.9681
	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	MRPS9	Measured	Divided	7621.65	7792.73	1.02245
	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	no value	Squared	Subtracted	44316.2	43098.8	1217.4
	proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062]			Divided	44612.9	43384.1	1.02832
	protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]	PACSIN1	Ranked		201.469	199.1	1.0119
	rho interacting protein 3. [refseq;acc:nm_015134]	no value	Rooted		71.2429	73.1967	1.02742
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	SPHK2	Ranked	Subtracted	204.262	201.891	2.371
	zinc finger protein 407. [refseq;acc:nm_017757]	ZNF407	Measured		9143.31	9323.17	179.86
3987	block of proliferation 1. [swissprot;acc:q14137]	BOP1		Divided	8236.57	8421.4	1.02244
	gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488]	POFUT1	Ranked		201.469	199.1	1.0119
	heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082]	HSPB2	Squared		42167.8	41006.9	1.02831
	protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6]	PACSIN3	Ranked	Subtracted	201.469	199.1	2.369
	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	TRIOBP	Rooted	Divided	71.2429	73.1967	1.02742
	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	RALGDS		Subtracted	73.9992	75.9668	1.9676
	zinc finger protein 143 (sph-binding factor). [swissprot;acc:p52747]	ZNF143	Measured		9143.31	9323.17	179.86
	zinc finger protein 183. [swissprot;acc:o15541]	RNF113A	Squared		42032.5	40816.4	1216.1
3988	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	no value	Measured	Divided	7522.57	7691.21	1.02242
	coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250]	BICD2	Squared	Subtracted	43173.4	41958.5	1214.9
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	no value		Divided	45404.2	44155.8	1.02827

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.