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	Gene	description	Value Type	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	description	Value Type	red	green	network_comparison
419	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]	Measured	5493.1	6350.19	1.15603
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Ranked	233.539	253.197	1.08417
420	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	Squared	30924.3	37652.3	1.21756
	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	Ranked	233.539	253.197	1.08417
	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	Rooted	51.7959	56.9253	1.09903
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Measured	10235.2	11830.8	1.15589
421	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Rooted	50.4666	45.9317	1.09873
	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Squared	36933	44953.6	1.21717
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Ranked	223.202	205.9	1.08403
	vav-2 protein. [swissprot;acc:p52735]	Measured	6660.02	7697.78	1.15582
422	60s ribosomal protein l5. [swissprot;acc:p46777]	Rooted	50.4641	45.9293	1.09873
	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	Squared	25860	31475.4	1.21715
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Measured	5206.9	6010.04	1.15425
	ras-related protein rab-37. [swissprot;acc:q96ax2]	Ranked	240.287	260.193	1.08284
423	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Rooted	50.4663	45.9313	1.09873
	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	Measured	5207.03	6010.1	1.15423
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Ranked	240.287	260.193	1.08284
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Squared	36735.7	44689.6	1.21652
424	60s ribosomal protein l23a. [swissprot;acc:p29316]	Rooted	50.4703	45.9373	1.09868
	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]	Ranked	240.287	260.193	1.08284
	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	Squared	20259.5	24635.7	1.21601
	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	Measured	5207.78	6010.45	1.15413
425	40s ribosomal protein s20. [swissprot;acc:p17075]	Rooted	50.0161	45.5318	1.09849
	max protein. [swissprot;acc:p25912]	Ranked	227.828	210.561	1.082
	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	Squared	20258.6	24634.7	1.21601
	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Measured	3729.02	4301.58	1.15354
426	dynactin 4. [refseq;acc:nm_032486]	Ranked	233.142	252.253	1.08197
	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	Rooted	55.1073	60.5285	1.09838
	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Measured	5942.49	6853.15	1.15325
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Squared	20267.8	24644.8	1.21596
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Ranked	239.977	259.525	1.08146
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Rooted	54.4927	49.6125	1.09837
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Squared	25380.3	30835.9	1.21495
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Measured	11736.6	13531.9	1.15297
428	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Rooted	54.4927	49.6125	1.09837
	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	Ranked	253.852	234.808	1.0811
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Measured	3721.19	4288.17	1.15237
	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Squared	29101.9	35347	1.21459
429	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Rooted	54.4927	49.6125	1.09837
	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	Ranked	239.709	259.038	1.08064
	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Squared	29101.9	35347	1.21459
	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	Measured	6272.91	7226.06	1.15195
430	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Squared	29098.8	35342.6	1.21457
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Rooted	54.4927	49.6125	1.09837
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Measured	3804.09	4379.37	1.15123
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Ranked	227.748	210.888	1.07995
431	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	Measured	3849.94	4431.36	1.15102
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Rooted	54.4927	49.6125	1.09837
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared	29096	35338.7	1.21456
	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Ranked	236.245	255.113	1.07987

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.