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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 130 to 179 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
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]	Subtracted	187.457	243.678	56.221	
66	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Divided	267.136	336.077	1.25807	
66	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Subtracted	187.458	243.678	56.22	
67	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Divided	267.14	336.075	1.25805	
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	187.458	243.677	56.219	
68	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	Divided	267.139	336.075	1.25805	
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	187.462	243.673	56.211	
69	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	Divided	267.14	336.075	1.25805	
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	284.753	228.934	55.819	
70	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04899]	Divided	267.142	336.074	1.25804	
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]	Subtracted	188.688	242.742	54.054	
71	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04898]	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]	Subtracted	265.686	319.651	53.965	
72	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	Divided	267.144	336.073	1.25802	
72	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Subtracted	265.639	319.546	53.907	
73	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	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]	Subtracted	265.632	319.531	53.899	
74	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	288	362	1.25694	
74	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]	Subtracted	189.07	242.453	53.383	
75	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Divided	288	362	1.25694	
75	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [source:swissprot;acc:q8wxs5]	Subtracted	254.693	202.668	52.025	
76	db83 protein. [source:swissprot;acc:p57088]	Divided	288	362	1.25694	
76	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Subtracted	254.693	202.668	52.025	
77	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [source:swissprot;acc:q9y698]	Divided	254.692	202.668	1.2567	
77	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [source:swissprot;acc:q9y698]	Subtracted	254.692	202.668	52.024	
78	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	Subtracted	254.691	202.668	52.023	
78	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [source:swissprot;acc:q8wxs5]	Divided	254.693	202.668	1.2567	
79	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Divided	254.693	202.668	1.2567	
79	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Subtracted	254.614	202.646	51.968	
80	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]	Subtracted	294.053	242.562	51.491	
80	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	Divided	254.691	202.668	1.25669	
81	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Subtracted	252.371	202.016	50.355	
81	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Divided	254.614	202.646	1.25645	
82	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	Divided	267.636	335.359	1.25304	
82	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Subtracted	252.329	202.004	50.325	
83	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Subtracted	252.309	201.998	50.311	
83	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Divided	88.2482	110.265	1.24949	
84	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Divided	88.2482	110.265	1.24949	
84	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Subtracted	252.296	201.995	50.301	
85	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Divided	88.2482	110.265	1.24949	
85	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	Subtracted	296.677	247.559	49.118	
86	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Subtracted	335	286	49	
86	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Divided	88.2482	110.265	1.24949	
87	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	Subtracted	249.663	298.263	48.6	
87	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Divided	88.2482	110.265	1.24949	
88	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Divided	88.2482	110.265	1.24949	
88	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	Subtracted	249.663	298.263	48.6	
89	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Divided	88.2482	110.265	1.24949	
89	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	Subtracted	249.663	298.263	48.6	
90	necdin. [source:swissprot;acc:q99608]	Divided	88.2482	110.265	1.24949	

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/