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 1294 to 1343 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
647	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	Subtracted	214.257	202.125	12.132
648	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]			202.132	12.125
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Divided	218.227	206.078	1.05895
649	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]		233.725	220.751	1.05877
	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	Subtracted	214.257	202.132	12.125
650	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]			202.135	12.122
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Divided	228.986	216.276	1.05877
651	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]		233.725	220.751
	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	Subtracted	214.256	202.139	12.117
652	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	Divided	248.994	235.255	1.0584
653	dok-like protein. [refseq;acc:nm_024872]		216.504	204.622	1.05807
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Subtracted	214.256	202.139	12.117
654	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Divided	216.504	204.622	1.05807
	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	Subtracted	214.256	202.139	12.117
655	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Divided	216.504	204.622	1.05807
	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	Subtracted	214.256	202.14	12.116
656	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Divided	216.504	204.622	1.05807
657	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]	Subtracted	214.256	202.14	12.116
	synapsin iii. [swissprot;acc:o14994]	Divided	229.072	216.576	1.0577
658	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]	Subtracted	214.256	202.14	12.116
659	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]
	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3]	Divided	229.072	216.576	1.0577
660	actin binding lim protein 2. [refseq;acc:nm_032432]
	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]	Subtracted	214.256	202.14	12.116
661	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]
	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]	Divided	229.072	216.576	1.0577
662	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]	Subtracted	214.256	202.14	12.116
	synapsin ii. [swissprot;acc:q92777]	Divided	229.072	216.576	1.0577
663	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	Subtracted	214.256	202.141	12.115
664	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]	Divided	229.072	216.576	1.0577
	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]	Subtracted	214.256	202.141	12.115
665	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]	Divided	229.072	216.576	1.0577
	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	Subtracted	214.254	202.166	12.088
666	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]		250.465	238.38	12.085
	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]	Divided	229.072	216.576	1.0577
667	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Subtracted	250.465	238.38	12.085
668	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	Divided	229.072	216.576	1.0577
	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	Subtracted	244.495	232.419	12.076
669	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]		232.601	244.534	11.933
	synapsin i (brain protein 4.1). [swissprot;acc:p17600]	Divided	229.072	216.576	1.0577
670	autoantigen ngp-1. [swissprot;acc:q13823]		250.302	236.817	1.05694
	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]	Subtracted	232.601	244.534	11.933
671	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Divided	210.739	199.398	1.05688
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Subtracted	232.601	244.534	11.933
672	dok-like protein. [refseq;acc:nm_024872]		216.504	204.622	11.882

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.