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

Results: HTML CSV LaTeX

Showing element 25 to 74 of 3228 in total

Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

description	Rank	red	green	network_comparison	
26s protease regulatory subunit 7 (mss1 protein). [source:swissprot;acc:p35998]	2395	218.192	219.014	1.00377	
26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [source:swissprot;acc:p47210]	1637	202.358	199.408	1.01479	
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [source:swissprot;acc:q92524]	2478	216.177	216.801	1.00289	
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [source:swissprot;acc:q99460]	2368	218.555	219.434	1.00402	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	2269	217.419	218.627	1.00556	
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [source:swissprot;acc:o00231]	2367	217.589	218.475	1.00407	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	2316	217.241	218.311	1.00493	
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [source:swissprot;acc:q9unm6]	2329	217.112	218.116	1.00462	
26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [source:swissprot;acc:q13200]	2175	210.209	208.808	1.00671	
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [source:swissprot;acc:o43242]	2440	217.645	218.376	1.00336	
26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [source:swissprot;acc:p55036]	1432	220.987	225.468	1.02028	
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [source:swissprot;acc:q15008]	2432	215.807	216.556	1.00347	
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [source:swissprot;acc:p51665]	2355	217.232	218.162	1.00428	
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [source:swissprot;acc:p48556]	2525	215.835	216.341	1.00234	
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [source:swissprot;acc:o00233]	2620	215.615	215.91	1.00137	
26s proteasome-associated pad1 homolog. [source:refseq;acc:nm_005805]	2150	217.871	219.366	1.00686	
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [source:swissprot;acc:o14653]	810	212.386	221.785	1.04425	
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	325	243.944	268.195	1.09941	
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [source:swissprot;acc:q9y3d3]	2212	224.411	225.854	1.00643	
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	23	58	44	1.31818	
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [source:swissprot;acc:q9nvs2]	1659	217.925	214.826	1.01443	
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [source:swissprot;acc:q9byn8]	2675	214.893	215.108	1.001	
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	407	239.75	260.544	1.08673	
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [source:refseq;acc:nm_025193]	3147	0.00001	0.00001	1	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	2756	0.00001	0.00001	1	
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [source:swissprot;acc:p14060]	2802	0.00001	0.00001	1	
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [source:swissprot;acc:p04035]	2303	191.567	192.542	1.00509	
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]	3180	0.00001	0.00001	1	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	2189	209.54	208.162	1.00662	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1852	196.008	198.154	1.01095	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	2300	191.563	192.541	1.00511	
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	1025	205.632	199.266	1.03195	
3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [source:swissprot;acc:p18405]	1083	220.118	213.685	1.03011	
3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [source:swissprot;acc:p31213]	1084	220.118	213.685	1.03011	
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [source:swissprot;acc:o15530]	897	272.878	283.472	1.03882	
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [source:swissprot;acc:q14318]	2358	198.181	197.346	1.00423	
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	1745	219.423	222.215	1.01272	
40s ribosomal protein s11. [source:swissprot;acc:p04643]	278	241.399	267.088	1.10642	
40s ribosomal protein s13. [source:swissprot;acc:q02546]	1722	220.899	223.813	1.01319	
40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	386	242.238	264.11	1.09029	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	304	242.339	266.986	1.1017	
40s ribosomal protein s15a. [source:swissprot;acc:p39027]	292	241.411	266.414	1.10357	
40s ribosomal protein s16. [source:swissprot;acc:p17008]	391	241.828	263.62	1.09011	
40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	387	242.238	264.11	1.09029	
40s ribosomal protein s19. [source:swissprot;acc:p39019]	861	234.025	224.958	1.04031	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	344	241.625	265.136	1.0973	
40s ribosomal protein s20. [source:swissprot;acc:p17075]	342	243.5	267.21	1.09737	
40s ribosomal protein s21. [source:swissprot;acc:p35265]	790	224.244	234.511	1.04578	
40s ribosomal protein s23. [source:swissprot;acc:p39028]	324	243.944	268.195	1.09941	
40s ribosomal protein s24 (s19). [source:swissprot;acc:p16632]	1690	224.091	227.184	1.0138	

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/