Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 Interaction Map Network Comparison Type red Filtered green network_comparison

Results: HTML CSV LaTeX

Showing element 501 to 550 of 29840 in total

Interaction Map	High confidence

Rank	Value Type	description	Network Comparison Type	red	Filtered	green	network_comparison	
32	Ranked	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04899]	Subtracted	267.142	1	336.074	68.932	
32	Ranked	importin 9. [source:refseq;acc:nm_018085]	Divided	13292.2	0	8691.76	1.52929	
32	Ranked	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [source:swissprot;acc:q9y2t4]	Divided	187.462	1	243.673	1.29985	
32	Ranked	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Subtracted	13884.4	0	19014.6	5130.2	
32	Squared	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Divided	9924.76	1	25146.6	2.53372	
32	Squared	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Subtracted	106226	1	192141	85915	
32	Squared	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [source:swissprot;acc:p11086]	Divided	76.8994	0	4.57302	16.8159	
32	Squared	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	Subtracted	19892.6	0	27221.2	7328.6	
32	Rooted	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	Divided	26.0288	1	43.1914	1.65937	
32	Rooted	gbp protein isoform a. [source:refseq;acc:nm_017870]	Subtracted	23.9771	1	42.4773	18.5002	
32	Rooted	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Subtracted	0	0	9.43398	9.43398	
32	Rooted	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	Divided	24.0391	0	11.258	2.13529	
33	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Divided	1835.3	1	896.972	2.04611	
33	Measured	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	Divided	12.6208	0	39.8063	3.15402	
33	Measured	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Subtracted	23693.7	1	18263	5430.7	
33	Measured	protein cgi-147. [source:swissprot;acc:q9y3e5]	Subtracted	8396.12	0	9192.38	796.26	
33	Ranked	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04898]	Subtracted	267.144	1	336.073	68.929	
33	Ranked	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	Divided	13292.2	0	8691.76	1.52929	
33	Ranked	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	Divided	188.688	1	242.742	1.28647	
33	Ranked	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Subtracted	15264	0	20387	5123	
33	Squared	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	Subtracted	29812	0	36822.7	7010.7	
33	Squared	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	Divided	76.8994	0	4.57302	16.8159	
33	Squared	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Subtracted	106226	1	192141	85915	
33	Squared	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Divided	9924.76	1	25146.6	2.53372	
33	Rooted	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402]	Divided	12.3693	0	25.7294	2.0801	
33	Rooted	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	Subtracted	61.6393	0	70.9983	9.359	
33	Rooted	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Subtracted	25.6987	1	43.561	17.8623	
33	Rooted	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	Divided	26.0288	1	43.1914	1.65937	
34	Measured	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	Subtracted	4131.06	0	3340.03	791.03	
34	Measured	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	Divided	143	0	47	3.04255	
34	Measured	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Divided	1836.71	1	907.546	2.02382	
34	Measured	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Subtracted	23693.7	1	18263	5430.7	
34	Ranked	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402]	Subtracted	11543	0	6812	4731	
34	Ranked	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	Subtracted	267.144	1	336.073	68.929	
34	Ranked	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	Divided	11284	0	17173.8	1.52196	
34	Ranked	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [source:swissprot;acc:p30153]	Divided	189.07	1	242.453	1.28235	
34	Squared	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Divided	9924.76	1	25146.6	2.53372	
34	Squared	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	Subtracted	79383.4	0	72701	6682.4	
34	Squared	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	Divided	0.0435834	0	0.697197	15.9968	
34	Squared	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Subtracted	106226	1	192141	85915	
34	Rooted	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Subtracted	140.508	1	122.878	17.63	
34	Rooted	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Divided	40.2812	1	24.3678	1.65305	
34	Rooted	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [source:swissprot;acc:p11086]	Divided	23.8747	0	11.7898	2.02503	
34	Rooted	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Subtracted	3.16228	0	12.49	9.32772	
35	Measured	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	Divided	459.5	0	1377	2.99674	
35	Measured	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Subtracted	1603	0	898	705	
35	Measured	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Divided	1836.71	1	907.564	2.02378	
35	Measured	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Subtracted	23693.7	1	18263	5430.7	
35	Ranked	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	Subtracted	267.636	1	335.359	67.723	
35	Ranked	importin 9. [source:refseq;acc:nm_018085]	Subtracted	13292.2	0	8691.76	4600.44	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/