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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 532 to 581 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	Filtered	red	green	network_comparison
67	Ranked	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	0	10793.5	14291.5	1.32408
	Squared	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]		608.191	190.865	3.1865
		melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	1	219048	129762	1.68808
	Rooted	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	0	11.0051	15.3166	1.39177
		myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	1	63.8686	47.2654	1.35128
68	Measured	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		6475.5	10307.5	1.59177
		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	0	198.964	351.772	1.76802
	Ranked	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	1	267.139	336.075	1.25805
		purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	0	8932.56	11823.3	1.32362
	Squared	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	1	219048	129762	1.68808
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	31.36	0.00001	3136000
	Rooted	alpha crystallin a chain. [swissprot;acc:p02489]		6.22183	8.63381	1.38766
		glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	1	63.8686	47.2654	1.35128
69	Measured	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	0	1593	2804	1.7602
		spermatogenesis associated 6. [refseq;acc:nm_019073]	1	6475.5	10307.5	1.59177
	Ranked	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	0	7704.7	10174.1	1.32051
		guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	1	267.14	336.075	1.25805
	Squared	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		219048	129762	1.68808
		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	0	16.2406	50.7408	3.12432
	Rooted	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]		18.7392	13.5207	1.38596
		neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	1	27.9136	37.2872	1.33581
70	Measured	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		6475.5	10307.5	1.59177
		importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	0	607	1068	1.75947
	Ranked	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	1	267.142	336.074	1.25804
		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	0	13975.7	10593.2	1.31931
	Squared	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]		600.627	1860.93	3.09831
		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	1	219048	129762	1.68808
	Rooted	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]		27.9136	37.2872	1.33581
		enigma protein; lim domain protein. [refseq;acc:nm_005451]	0	10.4569	7.5456	1.38583
71	Measured	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	1	4556.78	2945.26	1.54716
		ubiquitin protein ligase. [refseq;acc:nm_130466]	0	620	352.75	1.75762
	Ranked	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	1	267.144	336.073	1.25802
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	0	4338.65	5700.79	1.31395
	Squared	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]		87.2069	269.97	3.09574
		melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	1	219048	129762	1.68808
	Rooted	doc-1 related protein (doc-1r). [swissprot;acc:o75956]		27.9136	37.2872	1.33581
		transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	0	22.1933	16.1491	1.37427
72	Measured	60s ribosomal protein l21. [swissprot;acc:p46778]		572	992.083	1.73441
		uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	1	4556.79	2945.28	1.54715
	Ranked	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]		267.144	336.073	1.25802
		putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	0	4119	5397	1.31027
	Squared	fos-related antigen 2. [swissprot;acc:p15408]		6691.06	2188.28	3.05768
		melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	1	219048	129762	1.68808
	Rooted	importin 9. [refseq;acc:nm_018085]	0	21.8651	29.828	1.36418
		neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	1	27.9136	37.2872	1.33581
73	Measured	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	0	65.2968	37.693	1.73233
		serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	1	4556.83	2945.38	1.54711
	Ranked	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		288	362	1.25694
		phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	0	4119	5397	1.31027
	Squared	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	1	219048	129762	1.68808

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.