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 563 to 612 of 3228 in total

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

Rank	description	red	green	network_comparison
563	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	5480.24	6222.04	1.13536
564	transforming protein rhoa (h12). [swissprot;acc:p06749]
565	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	10434.4	11846.2	1.1353
566	autoantigen ngp-1. [swissprot;acc:q13823]	3766.14	4274.79	1.13506
567	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316]	10264.9	9043.51
568	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5]	4134.77	4691.24	1.13458
569	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]
570	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]
571	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]
572	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]
573	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	6739.43	7644.55	1.1343
574	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	6739.61	7644.58	1.13428
575	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	6739.63	7644.59	1.13427
576	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	6739.7	7644.6	1.13426
577	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	6739.81	7644.62	1.13425
578	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
579	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	6739.82
580	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	6739.83	7644.63
581	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]	6739.82
582	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]		7644.62
583	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	6739.81
584	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]	6739.82	7644.63
585	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
586	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	6739.81	7644.62
587	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]	6739.83	7644.63
588	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
589	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	6739.85		1.13424
590	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]
591	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	6740.5	7644.76	1.13415
592	histone h2b.c (h2b/c). [swissprot;acc:q99880]	3946.32	4475.47	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]
595	histone h2b. [refseq;acc:nm_175055]
596	histone h2b.s (h2b/s). [swissprot;acc:p57053]
597	histone h2b.d (h2b/d). [swissprot;acc:q99877]
598	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]
599	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
600	histone h2b.e (h2b/e). [swissprot;acc:q99879]
601	symplekin. [swissprot;acc:q92797]	15213.4	13418.1	1.1338
602	ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	4864.66	5514.87	1.13366
603	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]
604	vinculin (metavinculin). [swissprot;acc:p18206]	5958.23	6743.37	1.13177
605	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	6143.52	6950.75	1.1314
606	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194]	6148.94	6955.76	1.13121
607	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	14976.4	13246.6	1.13058
608	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	4510.61	5098.74	1.13039
609	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	3886.62	3438.82	1.13022
610	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	8430.03	9518.11	1.12907
611	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	5148.71	5811.74	1.12878
612	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	3975.77	4485.05	1.1281

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.