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 2544 to 2593 of 3228 in total

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

Rank	description	red	green	network_comparison
2544	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044]	6239.69	6378.35	1.02222
2545	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	8285.65	8107.49	1.02197
2546	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]	4763.99	4868.66
2547	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	3370.46	3444.18	1.02187
2548	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	4725.79	4824.4	1.02087
2549	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]
2550	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
2551	sorting nexin 17. [swissprot;acc:q15036]
2552	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	4884.35	4985.78	1.02077
2553	ras-related protein rab-37. [swissprot;acc:q96ax2]	3852.99	3775.86	1.02043
2554	ras-related protein rab-26. [swissprot;acc:q9ulw5]
2555	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
2556	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	4883.73	4982.88	1.0203
2557	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	5291.65	5187.78	1.02002
2558	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
2559	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]
2560	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
2561	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]
2562	cgthba protein (-14 gene protein). [swissprot;acc:q12980]
2563	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]
2564	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	3964.71	4042.75	1.01968
2565	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
2566	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]
2567	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]
2568	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
2569	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
2570	homeobox protein barh-like 2. [swissprot;acc:q9umq3]
2571	kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872]	7056.13	7194.65	1.01963
2572	zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78]	7056.42	7194.87	1.01962
2573	peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628]	7056.58	7194.99	1.01961
2574	katanin p60 subunit a 1. [refseq;acc:nm_007044]	4327.94	4248.77	1.01863
2575	rho interacting protein 3. [refseq;acc:nm_015134]	5608.38	5712.59	1.01858
2576	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	5608.22	5712.39	1.01857
2577	translin. [swissprot;acc:q15631]	4979.44	5071.53	1.01849
2578	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
2579	polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]
2580	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	4331.39	4252.8	1.01848
2581	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	4570.81	4654.97	1.01841
2582	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	3899.28	3829.53	1.01821
2583	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	3926.4	3857.88	1.01776
2584	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398]	4180.32	4253.46	1.0175
2585	rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480]
2586	map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]
2587	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]
2588	meiotic recombination protein spo11. [swissprot;acc:q9y5k1]
2589	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	7181.3	7057.99	1.01747
2590	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	7551.88	7422.68	1.01741
2591	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	7550.12	7422.01	1.01726
2592	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	7169.01	7047.98	1.01717
2593	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	4921.84	5005.06	1.01691

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.