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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

Results: HTML CSV LaTeX

Showing element 6408 to 6457 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	Value Type	description	network_comparison	red	green
801	Subtracted	Rooted	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]	4.0968	65.0565	69.1533
802	Divided	Measured	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	1.11047	6455.66	7168.82
		Ranked	testis-specific protein tex28. [swissprot;acc:o15482]	1.04425	212.386	221.785
		Squared	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	1.16319	20131.3	23416.5
		Rooted	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	1.06474	54.6759	51.3516
	Subtracted	Measured	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	611.163	779.167	1390.33
		Ranked	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	9.399	212.386	221.785
		Squared	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	3973.1	19987.6	23960.7
		Rooted	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	4.0913	82.1841	86.2754
803	Divided	Measured	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	1.11045	6455.02	7167.96
		Ranked	similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]	1.04425	212.386	221.785
		Squared	bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814]	1.16308	22573.3	26254.5
		Rooted	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	1.06474	54.6759	51.3516
	Subtracted	Measured	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	611.163	779.167	1390.33
		Ranked	syntaxin 1b. [swissprot;acc:q15531]	9.399	212.386	221.785
		Squared	transforming protein rhoc (h9). [swissprot;acc:p08134]	3973.1	19987.6	23960.7
		Rooted	calsyntenin-1 precursor. [swissprot;acc:o94985]	4.0913	82.1841	86.2754
804	Divided	Measured	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9]	1.11036	6770.78	7517.97
		Ranked	a kindred of iglon. [refseq;acc:nm_173808]	1.04425	212.386	221.785
		Squared	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	1.16302	24954.5	29022.6
		Rooted	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	1.0646	74.3877	79.1931
	Subtracted	Measured	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	611.163	779.167	1390.33
		Ranked	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	9.399	212.386	221.785
		Squared	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]	3973.1	19987.6	23960.7
		Rooted	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	4.0913	82.1841	86.2754
805	Divided	Measured	60s ribosomal protein l39. [swissprot;acc:p02404]	1.11003	4708.61	5226.71
		Ranked	ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]	1.04425	212.386	221.785
		Squared	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	1.16284	15384.8	17890
		Rooted	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	1.0645	74.3557	79.1513
	Subtracted	Measured	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	611.163	779.167	1390.33
		Ranked	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]	9.399	212.386	221.785
		Squared	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	3973.1	19987.6	23960.7
		Rooted	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	4.0913	82.184	86.2753
806	Divided	Measured	60s ribosomal protein l18a. [swissprot;acc:q02543]	1.11003	4708.61	5226.71
		Ranked	inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]	1.04425	212.386	221.785
		Squared	inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218]	1.16278	25555.4	29715.4
		Rooted	40s ribosomal protein s26. [swissprot;acc:p02383]	1.06435	62.4161	58.6426
	Subtracted	Measured	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	611.163	779.167	1390.33
		Ranked	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	9.326	267.447	276.773
		Squared	transforming protein rhoa (h12). [swissprot;acc:p06749]	3973.1	19987.6	23960.7
		Rooted	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	4.0913	82.184	86.2753
807	Divided	Measured	40s ribosomal protein s19. [swissprot;acc:p39019]	1.11003	4708.61	5226.71
		Ranked	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	1.04425	212.386	221.785
		Squared	inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732]	1.16277	25560.1	29720.6
		Rooted	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	1.06435	62.416	58.6426
	Subtracted	Measured	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	611.163	779.167	1390.33
		Ranked	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102]	9.275	218.521	227.796
		Squared	mad protein (max dimerizer). [swissprot;acc:q05195]	3965.6	17248.4	21214
		Rooted	gk001 protein. [refseq;acc:nm_020198]	4.0913	82.184	86.2753
808	Divided	Measured	60s ribosomal protein l31. [swissprot;acc:p12947]	1.11003	4708.61	5226.71

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.