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 600 to 649 of 3228 in total

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

red	green	Rank	description	network_comparison
3586.32	3414.42	2185	60s ribosomal protein l12. [swissprot;acc:p30050]	1.05035
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
3619.07	3461.21	2306	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	1.04561
3620.77	4763.34	136	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	1.31556
		137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]
3624.59	3463.37	2255	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	1.04655
3626.38	3734.8	2486	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	1.0299
3629.21	3467.48	2253	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	1.04664
3633.14	3754.96	2445	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	1.03353
3633.74	3473.68	2264	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	1.04608
3634.59	3756.67	2443	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	1.03359
3637.47	3435.61	2008	40s ribosomal protein s15a. [swissprot;acc:p39027]	1.05876
3639.65	3459.64	2169	60s ribosomal protein l5. [swissprot;acc:p46777]	1.05203
3640.58	3688.96	2634	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	1.01329
3641.4	3462.96	2173	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	1.05153
3641.45	3463.02	2174	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	1.05152
3641.62	3461.4	2167	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	1.05207
3641.89	4236.95	392	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	1.16339
3642.13	3463.88	2175	60s ribosomal protein l23a. [swissprot;acc:p29316]	1.05146
3646.01	3449.54	2039	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	1.05696
3650.02	3502.81	2375	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	1.04203
3650.78	3484.91	2226	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	1.0476

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.