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

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Showing element 580 to 629 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

red	green	Rank	description	network_comparison
3559.49	3360.39	1988	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	1.05925
3560.24	3364.84	2023	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	1.05807
3560.63	3381.34	2152	40s ribosomal protein s23. [swissprot;acc:p39028]	1.05302
		2153	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
3568.18	3675.65	2485	zinc finger protein 174 (aw-1). [swissprot;acc:q15697]	1.03012
3568.45	3675.97	2484	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	1.03013
3568.8	3676.38	2483	zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022]	1.03014
	3676.39	2481	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	1.03015
3568.84	3676.43	2477	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]
3568.95	3676.56	2480	zinc finger protein 305. [swissprot;acc:o43309]
3568.96	3676.57	2478	zinc finger protein 232. [swissprot;acc:q9uny5]
3568.99	3676.6	2479	zinc finger protein 99. [refseq;acc:nm_032164]
	3676.61	2482	zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771]
3569.06	3392.22	2163	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	1.05213
3569.07	3676.7	2476	zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6]	1.03016
3573.66	3682.14	2475	zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337]	1.03036
3582.57	3357.6	1756	40s ribosomal protein s29. [swissprot;acc:p30054]	1.067
3583.56	4194.95	369	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	1.17061
3586.3	3414.4	2186	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	1.05035
3586.31	3414.41	2187	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]
3586.32	3414.42	2185	60s ribosomal protein l12. [swissprot;acc:p30050]
3590.56	3422.6	2211	40s ribosomal protein s20. [swissprot;acc:p17075]	1.04907
3591.95	3375.34	1840	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	1.06417
		1841	fad synthetase. [refseq;acc:nm_025207]
		1842	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]
		1843	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]
		1844	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]
		1845	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]
		1846	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
3593.24	3375.93	1834	60s ribosomal protein l11. [swissprot;acc:p39026]	1.06437
3594.31	4169.95	412	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	1.16015
3598.08	3384.59	1894	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	1.06308
3598.55	3467.65	2417	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	1.03775
3600.99	3360.33	1588	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	1.07162
		1589	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
3601.97	3409.48	2051	60s ribosomal protein l26. [swissprot;acc:q02877]	1.05646
3602.25	3410.23	2065	60s ribosomal protein l35. [swissprot;acc:p42766]	1.05631
3602.75	3411.17	2068	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	1.05616
	3411.18	2067	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]
3612.45	3453.39	2265	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	1.04606
3614.07	3450.07	2234	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	1.04754
3614.08		2233	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]
3614.91	3423.89	2074	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	1.05579
		2075	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]
		2077	60s ribosomal protein l34. [swissprot;acc:p49207]
		2078	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]
		2079	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]
3617.81	3430.31	2114	60s ribosomal protein l3-like. [swissprot;acc:q92901]	1.05466
3618.02	3394.29	1798	60s ribosomal protein l32. [swissprot;acc:p02433]	1.06591
3618.46	3402.09	1873	40s ribosomal protein s11. [swissprot;acc:p04643]	1.0636

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.