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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 16530 to 16579 of 66312 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison
1034	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	Ranked	Subtracted	High confidence	229.442	235.974	6.532
	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]	Squared			22271.9	25656.8	3384.9
	heat shock cognate 71 kda protein. [swissprot;acc:p11142]	Measured			6437.99	6969.67	531.68
	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]	Squared	Divided	Low confidence	43303.1	41335	1.04761
	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]	Rooted	Subtracted		71.9157	74.7255	2.8098
	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155]	Ranked	Divided		202.723	197.922	1.02426
	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]		Subtracted		201.037	196.277	4.76
	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]	Squared	Divided	High confidence	31994	36719.6	1.1477
	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266]	Measured			6152.88	6732.12	1.09414
	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	Ranked			186.551	180.837	1.0316
	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]	Rooted	Subtracted		54.6759	51.3516	3.3243
	transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403]		Divided		58.8683	61.9622	1.05256
	u5 snrnp-associated 102 kda protein (u5-102 kda protein). [swissprot;acc:o94906]	Measured		Low confidence	7721.24	8013.26	1.03782
	ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974]	Rooted			71.2119	73.9796	1.03887
	zinc finger protein 132. [swissprot;acc:p52740]	Squared	Subtracted		56615.7	54513.3	2102.4
1035	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	Ranked			201.723	196.966	4.757
	alpha crystallin a chain. [swissprot;acc:p02489]	Measured			7095.99	7397.13	301.14
	alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5]	Squared		High confidence	22271.9	25656.8	3384.9
	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]	Ranked	Divided		221.682	228.68	1.03157
	beta-catenin (pro2286). [swissprot;acc:p35222]	Measured	Subtracted		5635.26	6166.09	530.83
	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	Rooted	Divided		60.6801	63.8644	1.05248
	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730]	Measured			5054.73	5530.23	1.09407
	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	Rooted	Subtracted	Low confidence	72.6663	75.4747	2.8084
	homeodomain-interacting protein kinase 2 (ec 2.7.1.-). [swissprot;acc:q9h2x6]	Squared	Divided		46699.9	44577.6	1.04761
	limkain b1. [refseq;acc:nm_019081]			High confidence	31994	36719.6	1.1477
	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]	Ranked		Low confidence	201.037	196.277	1.02425
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]		Subtracted	High confidence	229.441	235.972	6.531
	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]	Rooted	Divided	Low confidence	71.1927	73.9598	1.03887
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]		Subtracted	High confidence	54.6759	51.3516	3.3243
	vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106]	Measured	Divided	Low confidence	8054.13	8358.75	1.03782
	zinc finger protein 304. [swissprot;acc:q9hcx3]	Squared	Subtracted		56615.7	54513.3	2102.4
1036	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	Rooted		High confidence	51.6795	54.9937	3.3142
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Squared			20305.9	23689.4	3383.5
	coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618]	Ranked	Divided		171.341	176.746	1.03155
	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622]		Subtracted		207.719	214.236	6.517
	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098]	Measured	Divided	Low confidence	8023.84	8327.22	1.03781
	fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467]			High confidence	6077.65	6649.22	1.09404
	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	Rooted		Low confidence	71.1976	73.9632	1.03884
	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	Ranked	Subtracted		207.226	202.469	4.757
	phosphatidylinositol-4-phosphate 5-kinase, type i, gamma; phosphatidylinositol-4-phosphate 5-kinase i-gamma; diphosphoinositide kinase; type i pip kinase; ptdins(4)p-5-kinase. [refseq;acc:nm_012398]	Rooted			76.1308	78.9389	2.8081
	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]	Squared	Divided	High confidence	31994	36719.6	1.1477
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Measured	Subtracted		5910.54	6440.58	530.04
	ras-related protein rab-7. [swissprot;acc:p51149]	Ranked	Divided	Low confidence	199.336	194.616	1.02425
	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	Squared			47094.2	44954.3	1.0476
	vesicle trafficking protein sec22b. [refseq;acc:nm_004892]	Measured	Subtracted		7977.77	8278.9	301.13
	z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]	Rooted	Divided	High confidence	60.6801	63.8644	1.05248
	zinc finger protein 141. [swissprot;acc:q15928]	Squared	Subtracted	Low confidence	56615.7	54513.3	2102.4
1037	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]		Divided	High confidence	31994	36719.6	1.1477
	centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]			Low confidence	46721.6	44599	1.04759
	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	Rooted	Subtracted	High confidence	51.7273	55.0399	3.3126

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.