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

Results: HTML CSV LaTeX

Showing element 2575 to 2624 of 3228 in total

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

Rank	description	green	network_comparison	red
2575	rho interacting protein 3. [refseq;acc:nm_015134]	5712.59	1.01858	5608.38
2576	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	5712.39	1.01857	5608.22
2577	translin. [swissprot;acc:q15631]	5071.53	1.01849	4979.44
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]	4252.8	1.01848	4331.39
2581	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	4654.97	1.01841	4570.81
2582	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	3829.53	1.01821	3899.28
2583	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	3857.88	1.01776	3926.4
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]	4253.46	1.0175	4180.32
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]	7057.99	1.01747	7181.3
2590	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	7422.68	1.01741	7551.88
2591	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	7422.01	1.01726	7550.12
2592	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	7047.98	1.01717	7169.01
2593	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	5005.06	1.01691	4921.84
2594	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]
2595	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]
2596	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]
2597	ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669]	7970.2	1.01689	8104.84
2598	chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197]	7417.58	1.0163	7538.48
2599	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]	4438.77	1.01627	4367.69
2600	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622]	6283.8	1.01597	6185
2601	rad50 homolog isoform 1. [refseq;acc:nm_005732]	7110.74	1.01566	7222.12
2602	lim/homeobox protein lhx3. [swissprot;acc:q9ubr4]	7688.39	1.01541	7571.73
2603	lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290]	7689.04	1.01536	7572.69
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]	7689.81	1.01531	7573.83
2606	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	4517.54	1.01499	4450.84
2607	stromal interaction molecule 1 precursor. [swissprot;acc:q13586]	6476.19	1.01498	6380.61
2608	trap/mediator complex component trap25. [refseq;acc:nm_080651]	6476.18		6380.6
2609	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	6476.41		6380.84
2610	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]	6476.19		6380.61
2611	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	6476.18		6380.6
2612	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]	6476.19		6380.61
2613	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	6476.18		6380.6
2614	stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]	6476.19		6380.61
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]	6475.92		6380.32
2617	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4]	5683	1.01485	5599.85
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]	6916.14	1.01481	6815.24
2624	ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]

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.