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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 25824 in total

Filtered	1
Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
63	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Measured	Divided	4489.19	2765.82	1.6231	
63	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Ranked	Subtracted	260.532	204.309	56.223	
63	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Squared	Subtracted	189976	124480	65496	
63	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Measured	Subtracted	6475.5	10307.5	3832	
64	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Rooted	Divided	63.8686	47.2654	1.35128	
64	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Measured	Subtracted	6475.5	10307.5	3832	
64	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Ranked	Subtracted	260.532	204.309	56.223	
64	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Squared	Subtracted	144940	81169.7	63770.3	
64	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Measured	Divided	4489.19	2765.82	1.6231	
64	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Ranked	Divided	266.868	336.159	1.25965	
64	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Squared	Divided	219048	129762	1.68808	
64	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Rooted	Subtracted	137.446	120.823	16.623	
65	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Measured	Subtracted	22515.5	18702.6	3812.9	
65	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Rooted	Divided	63.8686	47.2654	1.35128	
65	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Ranked	Divided	267.136	336.077	1.25807	
65	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Squared	Divided	219048	129762	1.68808	
65	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Rooted	Subtracted	137.446	120.823	16.623	
65	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Squared	Subtracted	144912	81155	63757	
65	neuralized-like. [source:refseq;acc:nm_004210]	Measured	Divided	1657.68	2690.25	1.6229	
65	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). [source:swissprot;acc:q00007]	Ranked	Subtracted	187.457	243.678	56.221	
66	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Measured	Subtracted	17757.5	14008	3749.5	
66	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Rooted	Divided	63.8686	47.2654	1.35128	
66	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Ranked	Divided	267.136	336.077	1.25807	
66	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Squared	Divided	219048	129762	1.68808	
66	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Squared	Subtracted	144911	81154.7	63756.3	
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]	Measured	Divided	1991.03	3221.38	1.61795	
66	trophinin. [source:swissprot;acc:q12816]	Rooted	Subtracted	137.446	120.823	16.623	
66	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Ranked	Subtracted	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]	Rooted	Subtracted	63.8686	47.2654	16.6032	
67	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Measured	Divided	6475.5	10307.5	1.59177	
67	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Squared	Subtracted	144876	81136.5	63739.5	
67	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Ranked	Divided	267.14	336.075	1.25805	
67	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Squared	Divided	219048	129762	1.68808	
67	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Rooted	Divided	63.8686	47.2654	1.35128	
67	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Measured	Subtracted	17756.5	14007.3	3749.2	
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]	Ranked	Subtracted	187.458	243.677	56.219	
68	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Measured	Divided	6475.5	10307.5	1.59177	
68	cyclin g2. [source:swissprot;acc:q16589]	Measured	Subtracted	17738.6	13995.7	3742.9	
68	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Squared	Subtracted	139741	78454.6	61286.4	
68	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Rooted	Subtracted	63.8686	47.2654	16.6032	
68	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Rooted	Divided	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]	Ranked	Divided	267.139	336.075	1.25805	
68	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Squared	Divided	219048	129762	1.68808	
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]	Ranked	Subtracted	187.462	243.673	56.211	
69	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Measured	Subtracted	17738.5	13995.6	3742.9	
69	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Rooted	Subtracted	63.8686	47.2654	16.6032	
69	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	Ranked	Divided	267.14	336.075	1.25805	
69	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Squared	Divided	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]	Ranked	Subtracted	284.753	228.934	55.819	
69	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Rooted	Divided	27.9136	37.2872	1.33581	

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/