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

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Showing element 501 to 550 of 29840 in total

Interaction Map

: High confidence

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

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.

- http://analysis.yellowcouch.org/