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.

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

Results: HTML CSV LaTeX

Showing element 530 to 579 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
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	
69	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Squared	Subtracted	178263	118639	59624	
69	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Measured	Divided	6475.5	10307.5	1.59177	
70	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Measured	Divided	6475.5	10307.5	1.59177	
70	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Rooted	Divided	27.9136	37.2872	1.33581	
70	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Squared	Subtracted	129597	73157.5	56439.5	
70	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04899]	Ranked	Divided	267.142	336.074	1.25804	
70	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Squared	Divided	219048	129762	1.68808	
70	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Rooted	Subtracted	63.8686	47.2654	16.6032	
70	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	Measured	Subtracted	17738.5	13995.7	3742.8	
70	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]	Ranked	Subtracted	188.688	242.742	54.054	
71	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Squared	Subtracted	129597	73157.5	56439.5	
71	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Rooted	Divided	27.9136	37.2872	1.33581	
71	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Rooted	Subtracted	63.8686	47.2654	16.6032	
71	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04898]	Ranked	Divided	267.144	336.073	1.25802	
71	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Ranked	Subtracted	265.686	319.651	53.965	
71	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Squared	Divided	219048	129762	1.68808	
71	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]	Measured	Divided	4556.78	2945.26	1.54716	
71	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [source:swissprot;acc:q15172]	Measured	Subtracted	17738.5	13995.7	3742.8	
72	44050 protein. [source:refseq;acc:nm_178832]	Squared	Subtracted	148058	99628.4	48429.6	
72	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Measured	Subtracted	17710.9	13977.7	3733.2	
72	deltex 2. [source:refseq;acc:nm_020892]	Rooted	Subtracted	27.634	43.9629	16.3289	
72	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	Ranked	Divided	267.144	336.073	1.25802	
72	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Squared	Divided	219048	129762	1.68808	
72	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Rooted	Divided	27.9136	37.2872	1.33581	
72	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Ranked	Subtracted	265.639	319.546	53.907	
72	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Measured	Divided	4556.79	2945.28	1.54715	
73	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Rooted	Subtracted	27.7078	44.017	16.3092	
73	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Ranked	Divided	288	362	1.25694	
73	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Ranked	Subtracted	265.632	319.531	53.899	

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/