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

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Showing element 1675 to 1724 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	red	green	network_comparison
419	Squared	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	24832.1	30242.8	1.21789
	Rooted	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	55.5489	50.535	1.09922
420	Measured	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	10235.2	11830.8	1.15589
	Ranked	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	233.539	253.197	1.08417
	Squared	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	30924.3	37652.3	1.21756
	Rooted	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	51.7959	56.9253	1.09903
421	Measured	vav-2 protein. [swissprot;acc:p52735]	6660.02	7697.78	1.15582
	Ranked	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	223.202	205.9	1.08403
	Squared	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	36933	44953.6	1.21717
	Rooted	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	50.4666	45.9317	1.09873
422	Measured	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	5206.9	6010.04	1.15425
	Ranked	ras-related protein rab-37. [swissprot;acc:q96ax2]	240.287	260.193	1.08284
	Squared	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	25860	31475.4	1.21715
	Rooted	60s ribosomal protein l5. [swissprot;acc:p46777]	50.4641	45.9293	1.09873
423	Measured	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	5207.03	6010.1	1.15423
	Ranked	ras-related protein rab-26. [swissprot;acc:q9ulw5]	240.287	260.193	1.08284
	Squared	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	36735.7	44689.6	1.21652
	Rooted	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	50.4663	45.9313	1.09873
424	Measured	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	5207.78	6010.45	1.15413
	Ranked	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]	240.287	260.193	1.08284
	Squared	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	20259.5	24635.7	1.21601
	Rooted	60s ribosomal protein l23a. [swissprot;acc:p29316]	50.4703	45.9373	1.09868
425	Measured	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	3729.02	4301.58	1.15354
	Ranked	max protein. [swissprot;acc:p25912]	227.828	210.561	1.082
	Squared	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	20258.6	24634.7	1.21601
	Rooted	40s ribosomal protein s20. [swissprot;acc:p17075]	50.0161	45.5318	1.09849
426	Measured	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	5942.49	6853.15	1.15325
	Ranked	dynactin 4. [refseq;acc:nm_032486]	233.142	252.253	1.08197
	Squared	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	20267.8	24644.8	1.21596
	Rooted	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	55.1073	60.5285	1.09838
427	Measured	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	11736.6	13531.9	1.15297
	Ranked	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	239.977	259.525	1.08146
	Squared	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	25380.3	30835.9	1.21495
	Rooted	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	54.4927	49.6125	1.09837
428	Measured	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	3721.19	4288.17	1.15237
	Ranked	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	253.852	234.808	1.0811
	Squared	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	29101.9	35347	1.21459
	Rooted	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	54.4927	49.6125	1.09837
429	Measured	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	6272.91	7226.06	1.15195
	Ranked	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	239.709	259.038	1.08064
	Squared	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	29101.9	35347	1.21459
	Rooted	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	54.4927	49.6125	1.09837
430	Measured	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	3804.09	4379.37	1.15123
	Ranked	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	227.748	210.888	1.07995
	Squared	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	29098.8	35342.6	1.21457
	Rooted	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	54.4927	49.6125	1.09837
431	Measured	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	3849.94	4431.36	1.15102
	Ranked	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	236.245	255.113	1.07987
	Squared	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	29096	35338.7	1.21456
	Rooted	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	54.4927	49.6125	1.09837

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.