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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

description	Filtered	Value Type	Rank	green	red	network_comparison	
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	1	Squared	595	40434.8	34129.7	1.18474	
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	1	Rooted	751	71.4638	66.9738	1.06704	
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	1	Measured	686	7747.63	6920.69	1.11949	
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	1	Ranked	874	203.954	212.002	1.03946	
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	1	Squared	596	40434.5	34129.6	1.18473	
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	1	Rooted	749	71.4637	66.9737	1.06704	
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	1	Measured	692	7747.63	6920.69	1.11949	
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	1	Ranked	880	203.954	212.002	1.03946	
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	1	Squared	601	40434.5	34129.6	1.18473	
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	1	Rooted	756	71.4637	66.9737	1.06704	
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	1	Measured	690	7747.63	6920.69	1.11949	
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	1	Ranked	878	203.954	212.002	1.03946	
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	1	Squared	599	40434.5	34129.6	1.18473	
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	1	Rooted	754	71.4637	66.9737	1.06704	
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	1	Measured	1606	5606.53	5232.99	1.07138	
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	1	Ranked	1769	225.734	223.016	1.01219	
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	1	Squared	1192	24612.9	21639	1.13743	
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	1	Rooted	2302	60.5463	59.4004	1.01929	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	0	Measured	57	142.417	270.264	1.89769	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	0	Ranked	288	16053	14930.6	1.07517	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	0	Squared	65	15.1833	50.642	3.33538	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	0	Rooted	83	8.12243	10.9038	1.34243	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	1	Measured	1229	6509.74	5998.69	1.08519	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	1	Ranked	1021	214.409	221.278	1.03204	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	1	Squared	2161	32683.2	30116.4	1.08523	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	1	Rooted	981	65.3733	61.9129	1.05589	
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [source:swissprot;acc:p22557]	1	Measured	1910	7287.27	6858.84	1.06246	
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [source:swissprot;acc:p22557]	1	Ranked	2491	195.08	194.527	1.00284	
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [source:swissprot;acc:p22557]	1	Squared	786	31927.7	27407.7	1.16492	
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [source:swissprot;acc:p22557]	1	Rooted	2312	71.8706	70.5239	1.0191	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	0	Measured	287	808.929	726.245	1.11385	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	0	Ranked	412	8279.69	8546.06	1.03217	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	0	Squared	419	212.386	202.436	1.04915	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	0	Rooted	335	25.588	24.2756	1.05406	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	1	Measured	1915	7287.27	6858.84	1.06246	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	1	Ranked	2496	195.08	194.527	1.00284	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	1	Squared	791	31927.7	27407.7	1.16492	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	1	Rooted	2317	71.8706	70.5239	1.0191	
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [source:swissprot;acc:p49914]	1	Measured	1833	6572.85	6175.23	1.06439	
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [source:swissprot;acc:p49914]	1	Ranked	2754	210.642	210.638	1.00002	
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [source:swissprot;acc:p49914]	1	Squared	1635	30221.1	27290.4	1.10739	
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [source:swissprot;acc:p49914]	1	Rooted	2095	66.4806	64.8399	1.0253	
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	1	Measured	1115	6314.19	5795.13	1.08957	
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	1	Ranked	1921	219.386	221.607	1.01012	
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	1	Squared	941	30020.3	26005.2	1.1544	
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	1	Rooted	1362	64.0358	61.5231	1.04084	
54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	1	Measured	2028	9686.82	10243.4	1.05746	
54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	1	Ranked	2532	190.812	190.405	1.00214	
54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	1	Squared	353	57399.3	71383	1.24362	
54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	1	Rooted	2636	79.843	80.3593	1.00647	

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/