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

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

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.