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 2701 to 2750 of 3228 in total

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

Rank	description	red	green	network_comparison
2701	dynein light chain 2. [refseq;acc:nm_080677]	5239.33	5260	1.00395
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
2713	ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]
2714	inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]
2715	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	5332.98	5351.72
2716	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]
2717	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	5603.24	5583.64
2718	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]
2719	syntaxin 16 (syn16). [swissprot;acc:o14662]
2720	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
2721	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]
2722	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
2723	adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]
2724	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]
2725	syntaxin 1b. [swissprot;acc:q15531]
2726	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]	5332.98	5351.72
2727	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	5603.24	5583.64
2728	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
2729	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	5333	5351.61	1.00349
2730	myelin gene expression factor 2. [refseq;acc:nm_016132]	5214.9	5197.18	1.00341
2731	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	7913.63	7939.94	1.00332
2732	transcription factor relb (i-rel). [swissprot;acc:q01201]
2733	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]
2734	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
2735	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]	8991.87	9019.99	1.00313
2736	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	4887.59	4902.08	1.00296
2737	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	4486.83	4499.52	1.00283
2738	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]
2739	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]	4877.74	4890.64	1.00264
2740	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	4200.59	4210.94	1.00246
2741	sorting nexin 5. [swissprot;acc:q9y5x3]	5339.67	5327.2	1.00234
2742	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	10198.1	10174.3
2743	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	4824.49	4813.92	1.0022
2744	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	10143.6	10163.6	1.00197
2745	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	7746.61	7757.23	1.00137
2746	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	4188.5	4194.22
2747	putatative 28 kda protein. [refseq;acc:nm_020143]	4708.68	4702.58	1.0013
2748	syntaxin 6. [swissprot;acc:o43752]	5296.39	5301.11	1.00089
2749	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]	7776.91	7783.48	1.00084
2750	syntaxin 10 (syn10). [swissprot;acc:o60499]	5294.28	5298.42	1.00078

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.