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

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Showing element 2663 to 2712 of 3228 in total

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

Rank	description	red	green	network_comparison
2663	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	4608.54	4576.35	1.00703
2664	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	4608.91	4576.78	1.00702
2665	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	8936.97	8999.55	1.007
2666	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	4591.08	4621.88	1.00671
2667	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436]	4071.9	4099.01	1.00666
2668	iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399]	8222.61	8169.38	1.00652
2669	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	4336.58	4310.3	1.0061
2670	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	4336.62	4310.35	1.00609
2671	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	4338.79	4313.52	1.00586
2672	ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112]	7350.69	7390.45	1.00541
2673	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	7780.98	7741.14	1.00515
2674	sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864]
2675	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]
2676	atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]
2677	lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]
2678	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]
2679	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	5358.78	5384.44	1.00479
2680	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914]	5358.3	5383.94
2681	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177]	5358.31		1.00478
2682	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83]	5358.3	5383.93
2683	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153]
2684	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	5357.73	5383.33
2685	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	3953.53	3972.32	1.00475
2686	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
2687	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]
2688	oligophrenin 1. [swissprot;acc:o60890]
2689	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]	4113.79	4095.53	1.00446
2690	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]
2691	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]
2692	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]
2693	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
2694	60s ribosomal protein l18. [swissprot;acc:q07020]
2695	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	5176.92	5154.43	1.00436
2696	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]
2697	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]
2698	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	4163.36	4145.95	1.0042
2699	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	5356.83	5378.19	1.00399
2700	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	5239.33	5260	1.00395
2701	dynein light chain 2. [refseq;acc:nm_080677]
2702	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540]	8971.66	9006.92	1.00393
2703	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	8972.87	9007.71	1.00388
2704	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]	8980.12	9013.33	1.0037
2705	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	4137.61	4152.72	1.00365
2706	peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347]	8979.61	9012.31	1.00364
2707	prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675]
2708	j domain protein c21orf55. [swissprot;acc:q9nx36]	8979.78	9012.42	1.00363
2709	testis-specific protein tex28. [swissprot;acc:o15482]	5603.24	5583.64	1.00351
2710	similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]
2711	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]	5332.98	5351.72
2712	a kindred of iglon. [refseq;acc:nm_173808]	5603.24	5583.64

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.