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

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Showing element 762 to 811 of 3228 in total

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

green	Rank	description	red	network_comparison
4264.46	463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	3720.18	1.1463
4274.79	566	autoantigen ngp-1. [swissprot;acc:q13823]	3766.14	1.13506
4279.17	900	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	4713.58	1.10152
4288.17	428	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	3721.19	1.15237
4301.58	425	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	3729.02	1.15354
4310.3	2669	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	4336.58	1.0061
4310.35	2670	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	4336.62	1.00609
4310.89	447	pescadillo homolog 1. [swissprot;acc:o00541]	3751.14	1.14922
4313.52	2671	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	4338.79	1.00586
4315.06	452	zinc finger-like protein 9. [refseq;acc:nm_033414]	3760.8	1.14738
	453	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
	454	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
4315.95	445	ad24 protein. [refseq;acc:nm_022451]	3753.71	1.14978
4319.69	449	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	3761.59	1.14837
4322.87	444	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	3758.67	1.15011
4329.37	446	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	3766.03	1.14958
4334.66	2662	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	4300.46	1.00795
4336.92	2384	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	4164.96	1.04129
4337.01	2383	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	4164.76	1.04136
4346.98	460	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	3790.11	1.14693
4348.48	437	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	3779.92	1.15042
4348.59	470	block of proliferation 1. [swissprot;acc:q14137]	3796.24	1.1455
4352.56	2507	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	4243.44	1.02571
4362.61	144	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	3349.9	1.30231
4364.25	871	protein bap28. [swissprot;acc:q9h583]	3956.25	1.10313
4371.24	619	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	3879.99	1.12661
4379.37	430	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	3804.09	1.15123
4379.71	553	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	3853.64	1.13651
4388.74	469	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	3831.17	1.14554
4392.15	1624	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	4102.1	1.07071
	1625	zinc finger protein 277. [swissprot;acc:q9nrm2]
4409.22	465	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	3847.31	1.14605
	466	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
4426.74	542	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	3889.27	1.13819
	544	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]
	545	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]
4428.28	1212	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	4077.89	1.08592
4431.34	336	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	3751.3	1.18128
4431.36	431	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	3849.94	1.15102
4438.77	2599	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]	4367.69	1.01627
4439.07	515	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	3890.53	1.14099
4446.41	2631	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	4508.81	1.01403
4450.98	506	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	3893.85	1.14308
4457.66	923	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	4057.54	1.09861
4465.61	713	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	3996.81	1.11729
4470.47	2412	dynactin 4. [refseq;acc:nm_032486]	4644.04	1.03883
4474.3	791	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	4025.3	1.11154
4475.47	592	histone h2b.c (h2b/c). [swissprot;acc:q99880]	3946.32	1.13409
	593	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
	594	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]

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.