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 580 to 629 of 3228 in total

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

Rank	network_comparison	red	description	green
580	1.13425	6739.83	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	7644.63
581		6739.82	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
582			gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]	7644.62
583		6739.81	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]
584		6739.82	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]	7644.63
585			gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
586		6739.81	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	7644.62
587		6739.83	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]	7644.63
588			gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
589	1.13424	6739.85	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]
590			similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]
591	1.13415	6740.5	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	7644.76
592	1.13409	3946.32	histone h2b.c (h2b/c). [swissprot;acc:q99880]	4475.47
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	1.1338	15213.4	symplekin. [swissprot;acc:q92797]	13418.1
602	1.13366	4864.66	ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	5514.87
603			ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]
604	1.13177	5958.23	vinculin (metavinculin). [swissprot;acc:p18206]	6743.37
605	1.1314	6143.52	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	6950.75
606	1.13121	6148.94	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]	6955.76
607	1.13058	14976.4	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	13246.6
608	1.13039	4510.61	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]	5098.74
609	1.13022	3886.62	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	3438.82
610	1.12907	8430.03	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	9518.11
611	1.12878	5148.71	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	5811.74
612	1.1281	3975.77	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	4485.05
613			trinucleotide repeat containing 15. [refseq;acc:nm_015575]
614	1.12798	11222.2	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	9948.93
615			cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
616			catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]
617	1.12783	5162.52	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	5822.47
618	1.12703	7878.27	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	8879.08
619	1.12661	3879.99	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	4371.24
620	1.12605	6227.87	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	7012.9
621	1.12601	4115.39	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	4633.96
622	1.126	6228.42	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	7013.21
623		6228.39	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	7013.19
624			dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
625			disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]
626			putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]
627			limkain b1. [refseq;acc:nm_019081]
628			putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
629			cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]

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.