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

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Showing element 1051 to 1100 of 66312 in total

Filtered	1

Rank	description	Network Comparison Type	Interaction Map	Value Type	red	green	network_comparison	
66	mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [source:refseq;acc:nm_020749]	Divided	Low confidence	Ranked	221.902	200.783	1.10518	
66	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Divided	High confidence	Measured	1991.03	3221.38	1.61795	
66	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Divided	Low confidence	Squared	74803.9	94281	1.26038	
66	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	Divided	Low confidence	Measured	4900.7	5555.81	1.13368	
66	trophinin. [source:swissprot;acc:q12816]	Subtracted	High confidence	Rooted	137.446	120.823	16.623	
66	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Subtracted	High confidence	Ranked	187.458	243.678	56.22	
67	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Subtracted	High confidence	Rooted	63.8686	47.2654	16.6032	
67	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Divided	High confidence	Measured	6475.5	10307.5	1.59177	
67	brachyury protein (t protein). [source:swissprot;acc:o15178]	Divided	Low confidence	Rooted	61.687	68.2003	1.10559	
67	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Subtracted	High confidence	Squared	144876	81136.5	63739.5	
67	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	Subtracted	Low confidence	Rooted	52.3425	45.0567	7.2858	
67	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Divided	High confidence	Ranked	267.14	336.075	1.25805	
67	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Divided	Low confidence	Measured	12176.9	13781.8	1.1318	
67	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [source:refseq;acc:nm_018433]	Subtracted	Low confidence	Measured	1927.68	2959.19	1031.51	
67	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Divided	High confidence	Squared	219048	129762	1.68808	
67	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Divided	High confidence	Rooted	63.8686	47.2654	1.35128	
67	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Subtracted	Low confidence	Squared	52172	64605	12433	
67	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	Subtracted	Low confidence	Ranked	195.817	215.516	19.699	
67	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Subtracted	High confidence	Measured	17756.5	14007.3	3749.2	
67	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Divided	Low confidence	Ranked	165.535	149.799	1.10505	
67	septin 6. [source:swissprot;acc:q14141]	Divided	Low confidence	Squared	74378.4	93531.9	1.25751	
67	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). [source:swissprot;acc:q00005]	Subtracted	High confidence	Ranked	187.458	243.677	56.219	
68	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	Divided	Low confidence	Ranked	239.692	217.005	1.10455	
68	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	Subtracted	Low confidence	Rooted	57.2649	64.3669	7.102	
68	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Divided	High confidence	Measured	6475.5	10307.5	1.59177	
68	cyclin g2. [source:swissprot;acc:q16589]	Subtracted	High confidence	Measured	17738.6	13995.7	3742.9	
68	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Subtracted	High confidence	Squared	139741	78454.6	61286.4	
68	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Subtracted	High confidence	Rooted	63.8686	47.2654	16.6032	
68	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Divided	High confidence	Rooted	63.8686	47.2654	1.35128	
68	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	Divided	High confidence	Ranked	267.139	336.075	1.25805	
68	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Divided	High confidence	Squared	219048	129762	1.68808	
68	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Subtracted	Low confidence	Squared	52168.6	64594.5	12425.9	
68	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Subtracted	Low confidence	Ranked	225.735	245.308	19.573	
68	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Divided	Low confidence	Measured	19498.1	17265.4	1.12932	
68	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Divided	Low confidence	Rooted	55.9786	61.8641	1.10514	
68	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Divided	Low confidence	Squared	27909.1	35068.7	1.25653	
68	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]	Subtracted	High confidence	Ranked	187.462	243.673	56.211	
68	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [source:swissprot;acc:p35030]	Subtracted	Low confidence	Measured	1972.65	2998.1	1025.45	
69	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Subtracted	Low confidence	Squared	63411.7	51068.8	12342.9	
69	amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [source:refseq;acc:nm_138817]	Divided	Low confidence	Measured	6991.78	7848.45	1.12253	
69	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Divided	Low confidence	Rooted	60.7884	67.1136	1.10405	
69	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Subtracted	High confidence	Measured	17738.5	13995.6	3742.9	
69	delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [source:swissprot;acc:p30038]	Divided	Low confidence	Squared	80538.1	64191.7	1.25465	
69	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Subtracted	High confidence	Rooted	63.8686	47.2654	16.6032	
69	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	Divided	High confidence	Ranked	267.14	336.075	1.25805	
69	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Divided	High confidence	Squared	219048	129762	1.68808	
69	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Subtracted	High confidence	Ranked	284.753	228.934	55.819	
69	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Subtracted	Low confidence	Rooted	59.0909	66.1317	7.0408	
69	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Divided	High confidence	Rooted	27.9136	37.2872	1.33581	
69	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Subtracted	High confidence	Squared	178263	118639	59624	

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/