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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Value Type Filtered Rank Gene description Network Comparison Type Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 38536 in total 
Value Type	Measured
Filtered	0
Network Comparison Type	Divided

Rank	description	Interaction Map	red	green	network_comparison	
251	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	High confidence	1225.08	1079.38	1.13498	
251	zinc finger protein 74 (hznf7). [source:swissprot;acc:q16587]	Low confidence	2352.49	1969.49	1.19447	
252	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	High confidence	1225.08	1079.38	1.13498	
252	zinc finger protein 285. [source:refseq;acc:nm_152354]	Low confidence	2352.38	1969.39	1.19447	
253	espin. [source:refseq;acc:nm_031475]	High confidence	1225.07	1079.38	1.13498	
253	zinc finger protein 117 (zinc finger protein hpf9) (fragment). [source:swissprot;acc:q03924]	Low confidence	2352.42	1969.43	1.19447	
254	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	High confidence	1318.22	1495.66	1.13461	
254	zinc finger protein 141. [source:swissprot;acc:q15928]	Low confidence	2352.42	1969.43	1.19447	
255	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	High confidence	1317.84	1495.22	1.1346	
255	zinc finger protein 197 (znf20). [source:swissprot;acc:o14709]	Low confidence	2352.58	1969.57	1.19446	
256	keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	High confidence	1224.65	1079.77	1.13418	
256	similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [source:refseq;acc:nm_033196]	Low confidence	2352.58	1969.57	1.19446	
257	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	High confidence	861.401	759.896	1.13358	
257	zinc finger protein mgc21738. [source:refseq;acc:nm_145044]	Low confidence	2352.73	1969.72	1.19445	
258	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	High confidence	1183.16	1337.54	1.13048	
258	zinc finger protein 257 (bone marrow zinc finger 4) (bmzf-4). [source:swissprot;acc:q9y2q1]	Low confidence	2352.89	1969.86	1.19445	
259	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	High confidence	1295.49	1463.51	1.1297	
259	krueppel-related zinc finger protein 1 (hkr1 protein). [source:swissprot;acc:p10072]	Low confidence	2352.89	1969.86	1.19445	
260	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	High confidence	1949.36	2202	1.1296	
260	zinc finger protein 354c; krab-zinc finger protein synten. [source:refseq;acc:nm_014594]	Low confidence	2352.69	1969.68	1.19445	
261	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	High confidence	1295.81	1463.55	1.12945	
261	zinc finger protein zfd25. [source:swissprot;acc:q9uii5]	Low confidence	2352.64	1969.64	1.19445	
262	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	High confidence	764.479	676.971	1.12926	
262	zinc finger protein 44 (zinc finger protein kox7) (gonadotropin inducible transcription repressor-2) (giot-2). [source:swissprot;acc:p15621]	Low confidence	2352.64	1969.64	1.19445	
263	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	High confidence	1843	1633	1.1286	
263	zinc finger protein 62; likely ortholog of mouse zinc finger protein 62. [source:refseq;acc:nm_152283]	Low confidence	2352.8	1969.78	1.19445	
264	pr-domain zinc finger protein 9. [source:swissprot;acc:q9nqv7]	Low confidence	2352.69	1969.68	1.19445	
264	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	High confidence	3336.48	2957.12	1.12829	
265	60s ribosomal protein l9. [source:swissprot;acc:p32969]	High confidence	1685.44	1894.01	1.12375	
265	zinc finger protein 221. [source:swissprot;acc:q9uk13]	Low confidence	2352.64	1969.64	1.19445	
266	aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	High confidence	1475.05	1312.91	1.1235	
266	zinc finger protein 73 (zinc finger protein 186) (hznf2). [source:swissprot;acc:o43830]	Low confidence	2353	1969.96	1.19444	
267	uncharacterized bone marrow protein bm033. [source:refseq;acc:nm_018452]	High confidence	1475.05	1312.91	1.1235	
267	zinc finger protein 354a (transcription factor 17) (zinc finger protein eznf). [source:swissprot;acc:o60765]	Low confidence	2352.95	1969.92	1.19444	
268	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [source:refseq;acc:nm_003902]	High confidence	604.529	538.094	1.12346	
268	zinc finger protein 155. [source:swissprot;acc:q12901]	Low confidence	2352.95	1969.92	1.19444	
269	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	High confidence	1217.92	1367.83	1.12309	
269	zinc finger protein 2. [source:refseq;acc:nm_021088]	Low confidence	2353.11	1970.07	1.19443	
270	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	High confidence	1217.96	1367.88	1.12309	
270	zinc finger protein 19 (zinc finger protein kox12) (fragment). [source:swissprot;acc:p17023]	Low confidence	2353.04	1970.01	1.19443	
271	histone h4. [source:swissprot;acc:p02304]	High confidence	21773.1	24446.3	1.12278	
271	zinc finger protein zfp-36 (fragment). [source:swissprot;acc:p16415]	Low confidence	2353.27	1970.21	1.19443	
272	60s ribosomal protein l15. [source:swissprot;acc:p39030]	High confidence	846.216	753.793	1.12261	
272	zinc finger protein 134. [source:swissprot;acc:p52741]	Low confidence	2353.38	1970.32	1.19442	
273	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	High confidence	1410.81	1582.65	1.1218	
273	zinc finger protein 337. [source:swissprot;acc:q9y3m9]	Low confidence	2353.42	1970.36	1.19441	
274	brain protein 16. [source:refseq;acc:nm_016458]	High confidence	2155.75	2418.14	1.12172	
274	zinc finger protein 358. [source:swissprot;acc:q9nw07]	Low confidence	2353.63	1970.55	1.1944	
275	novel c2h2 type zinc finger protein. [source:refseq;acc:nm_024325]	Low confidence	2353.74	1970.65	1.1944	
275	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [source:refseq;acc:nm_003075]	High confidence	717.401	804.725	1.12172	

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/