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

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Showing element 700 to 749 of 3228 in total

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

red	green	Rank	description	network_comparison
3803.04	3710.01	2523	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	1.02508
3804.09	4379.37	430	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	1.15123
3804.53	3705.05	2500	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	1.02685
3805.17	3718.86	2539	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	1.02321
3831.17	4388.74	469	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	1.14554
3843.06	3682.72	2360	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	1.04354
3847.31	4409.22	465	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	1.14605
		466	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
3847.84	3759.28	2533	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	1.02356
3849.94	4431.36	431	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	1.15102
3852.99	3775.86	2553	ras-related protein rab-37. [swissprot;acc:q96ax2]	1.02043
		2554	ras-related protein rab-26. [swissprot;acc:q9ulw5]
		2555	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
3853.64	4379.71	553	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	1.13651
3856.29	4624.15	305	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	1.19912
3858.52	4669.27	272	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	1.21012
3879.99	4371.24	619	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	1.12661
3880.5	3788.42	2530	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	1.02431
3886.62	3438.82	609	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	1.13022
3889.27	4426.74	542	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	1.13819
		544	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]
		545	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]
3890.53	4439.07	515	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	1.14099
3893.85	4450.98	506	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	1.14308
3899.28	3829.53	2582	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	1.01821
3926.4	3857.88	2583	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	1.01776
3933.74	3877.14	2628	40s ribosomal protein s9. [swissprot;acc:p46781]	1.0146
3936.2	3755.33	2220	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	1.04816
3936.33	3755.5	2221	thrombospondin 3 precursor. [swissprot;acc:p49746]	1.04815
3946.32	4475.47	592	histone h2b.c (h2b/c). [swissprot;acc:q99880]	1.13409
		593	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
		594	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
		595	histone h2b. [refseq;acc:nm_175055]
		596	histone h2b.s (h2b/s). [swissprot;acc:p57053]
		597	histone h2b.d (h2b/d). [swissprot;acc:q99877]
		598	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]
		599	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
		600	histone h2b.e (h2b/e). [swissprot;acc:q99879]
3953.53	3972.32	2685	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	1.00475
		2686	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
		2687	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]
		2688	oligophrenin 1. [swissprot;acc:o60890]
3956.25	4364.25	871	protein bap28. [swissprot;acc:q9h583]	1.10313
3964.71	4042.75	2564	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	1.01968
		2565	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
		2566	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]
		2567	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]
		2568	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
		2569	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
		2570	homeobox protein barh-like 2. [swissprot;acc:q9umq3]

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.