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 2600 to 2649 of 3228 in total

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

Rank	description	red	green	network_comparison
2600	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622]	6185	6283.8	1.01597
2601	rad50 homolog isoform 1. [refseq;acc:nm_005732]	7222.12	7110.74	1.01566
2602	lim/homeobox protein lhx3. [swissprot;acc:q9ubr4]	7571.73	7688.39	1.01541
2603	lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290]	7572.69	7689.04	1.01536
2604	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	7572.7
2605	lim/homeobox protein lhx4. [swissprot;acc:q969g2]	7573.83	7689.81	1.01531
2606	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	4450.84	4517.54	1.01499
2607	stromal interaction molecule 1 precursor. [swissprot;acc:q13586]	6380.61	6476.19	1.01498
2608	trap/mediator complex component trap25. [refseq;acc:nm_080651]	6380.6	6476.18
2609	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	6380.84	6476.41
2610	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]	6380.61	6476.19
2611	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	6380.6	6476.18
2612	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]	6380.61	6476.19
2613	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	6380.6	6476.18
2614	stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]	6380.61	6476.19
2615	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]
2616	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]	6380.32	6475.92
2617	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4]	5599.85	5683	1.01485
2618	cab2. [refseq;acc:nm_033419]
2619	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]
2620	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685]
2621	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]
2622	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]
2623	adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203]	6815.24	6916.14	1.01481
2624	ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]
2625	adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]
2626	insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663]	7424.26	7534.05	1.01479
2627	ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670]	7135.64	7240.5	1.0147
2628	40s ribosomal protein s9. [swissprot;acc:p46781]	3933.74	3877.14	1.0146
2629	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584]	4582.38	4649.17	1.01458
2630	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	3985.17	3928.38	1.01446
2631	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	4508.81	4446.41	1.01403
2632	histone h4. [swissprot;acc:p02304]	6072.17	6155.08	1.01365
2633	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	4000.73	3947.54	1.01347
2634	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	3640.58	3688.96	1.01329
2635	hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410]	7197.82	7291.66	1.01304
2636	ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	7017.82	7108.89	1.01298
2637	protein kinase nyd-sp25. [refseq;acc:nm_033516]	6527.56	6608.61	1.01242
2638	insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47]	7433.72	7525.14	1.0123
2639	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	6742.48	6814.18	1.01063
2640	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	5339.06	5395.25	1.01052
2641	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]	3377.01	3411.47	1.0102
2642	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	5935.71	5876.22	1.01012
2643	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
2644	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	9125.08	9217	1.01007
2645	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]	9128.19	9218.44	1.00989
2646	mct-1 protein. [refseq;acc:nm_014060]	4778.28	4732.13	1.00975
2647	mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
2648	tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399]	6365.03	6424.56	1.00935
2649	jm4 protein. [refseq;acc:nm_007213]	7133.06	7067.09	1.00933

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.