MK5 Microarray Data

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

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Showing element 501 to 550 of 38536 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided

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

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.