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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description Filtered Rank Value Type Gene Interaction Map green Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

description	Filtered	Rank	Value Type	green	red	network_comparison	
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [source:swissprot;acc:p52758]	1	2036	Rooted	68.7832	66.966	1.02714	
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [source:swissprot;acc:p52758]	1	2366	Ranked	202.529	203.353	1.00407	
15 kda selenoprotein precursor. [source:swissprot;acc:o60613]	1	914	Squared	34456.5	29772.1	1.15734	
15 kda selenoprotein precursor. [source:swissprot;acc:o60613]	1	1043	Measured	6933.36	6344.41	1.09283	
15 kda selenoprotein precursor. [source:swissprot;acc:o60613]	1	1334	Rooted	67.2624	64.5959	1.04128	
15 kda selenoprotein precursor. [source:swissprot;acc:o60613]	1	1948	Ranked	212.432	214.522	1.00984	
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [source:swissprot;acc:p15428]	1	2855	Measured	0.00001	0.00001	1	
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [source:swissprot;acc:p15428]	1	2855	Ranked	0.00001	0.00001	1	
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [source:swissprot;acc:p15428]	1	2855	Squared	0.00001	0.00001	1	
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [source:swissprot;acc:p15428]	1	2855	Rooted	0.00001	0.00001	1	
17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	1	1051	Ranked	217.998	211.449	1.03097	
17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	1	2377	Squared	27574.1	25809.5	1.06837	
17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	1	2521	Measured	6113.96	5964.17	1.02511	
17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	1	2642	Rooted	63.5847	63.9773	1.00617	
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	1	1393	Measured	6192.72	5743.36	1.07824	
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	1	1463	Rooted	62.6331	60.3015	1.03867	
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	1	1593	Squared	32473.8	29261.2	1.10979	
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	1	2007	Ranked	222.969	225.019	1.00919	
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [source:swissprot;acc:q02218]	1	1160	Ranked	214.041	208.55	1.02633	
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [source:swissprot;acc:q02218]	1	2426	Squared	28847.4	27135.1	1.0631	
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [source:swissprot;acc:q02218]	1	2506	Measured	6362.25	6200.39	1.0261	
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [source:swissprot;acc:q02218]	1	2700	Rooted	65.1252	65.3323	1.00318	
2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [source:swissprot;acc:p12694]	1	1484	Ranked	202.726	198.927	1.0191	
2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [source:swissprot;acc:p12694]	1	1699	Squared	31699.9	28693.8	1.10476	
2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [source:swissprot;acc:p12694]	1	2451	Measured	6957.34	6737.15	1.03268	
2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [source:swissprot;acc:p12694]	1	2716	Rooted	69.1987	69.1013	1.00141	
2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [source:swissprot;acc:p21953]	1	1389	Ranked	213.875	218.47	1.02148	
2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [source:swissprot;acc:p21953]	1	1579	Rooted	64.1938	61.9705	1.03588	
2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [source:swissprot;acc:p21953]	1	2288	Measured	6048.94	5783.76	1.04585	
2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [source:swissprot;acc:p21953]	1	2488	Squared	26643.2	25184.8	1.05791	
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	1	107	Measured	5843.51	4266.04	1.36977	
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	1	135	Rooted	66.6101	54.935	1.21253	
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	1	183	Ranked	198.011	228.306	1.153	
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	1	290	Squared	20126.8	15734.4	1.27916	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	0	19	Measured	26.1599	305.45	11.6763	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	0	26	Squared	0.344399	44.3683	128.828	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	0	26	Rooted	3.80565	13.7805	3.62106	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	0	47	Ranked	18499.2	12941.7	1.42943	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	1	3079	Measured	0.00001	0.00001	1	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	1	3079	Ranked	0.00001	0.00001	1	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	1	3079	Squared	0.00001	0.00001	1	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	1	3079	Rooted	0.00001	0.00001	1	
26s protease regulatory subunit 4 (p26s4). [source:swissprot;acc:q03527]	1	1521	Measured	6376.76	5938.56	1.07379	
26s protease regulatory subunit 4 (p26s4). [source:swissprot;acc:q03527]	1	1644	Squared	30104.4	27191.5	1.10713	
26s protease regulatory subunit 4 (p26s4). [source:swissprot;acc:q03527]	1	1870	Rooted	64.7621	62.901	1.02959	
26s protease regulatory subunit 4 (p26s4). [source:swissprot;acc:q03527]	1	2503	Ranked	216.137	215.581	1.00258	
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [source:swissprot;acc:p17980]	1	1496	Squared	30410	27295.8	1.11409	
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [source:swissprot;acc:p17980]	1	1527	Measured	6362.33	5926.76	1.07349	
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [source:swissprot;acc:p17980]	1	1916	Rooted	64.4831	62.679	1.02878	
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [source:swissprot;acc:p17980]	1	2474	Ranked	217.285	216.64	1.00298	

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/