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 1230 to 1279 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
615	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	Divided	214.257	202.132	1.05999
616	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Subtracted	177.698	190.24	12.542
617	carboxypeptidase b precursor. [refseq;acc:nm_020361]			190.239	12.541
	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	Divided	214.257	202.135	1.05997
618	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]		214.256	202.139	1.05994
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Subtracted	177.699	190.24	12.541
619	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Divided	214.256	202.139	1.05994
	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	Subtracted	206.274	218.792	12.518
620	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	Divided	214.256	202.14	1.05994
	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	Subtracted	206.274	218.792	12.518
621	60s acidic ribosomal protein p2. [swissprot;acc:p05387]		231.92	244.435	12.515
	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	Divided	214.256	202.14	1.05994
622	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
	synapsin iii. [swissprot;acc:o14994]	Subtracted	229.072	216.576	12.496
623	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]	Divided	214.256	202.14	1.05994
624	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]	Subtracted	229.072	216.576	12.496
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Divided	214.256	202.139	1.05994
625	actin binding lim protein 2. [refseq;acc:nm_032432]	Subtracted	229.072	216.576	12.496
	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]	Divided	214.256	202.14	1.05994
626	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]	Subtracted	229.072	216.576	12.496
627	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	Divided	214.256	202.139	1.05994
	synapsin ii. [swissprot;acc:q92777]	Subtracted	229.072	216.576	12.496
628	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]	Divided	214.256	202.14	1.05994
	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]	Subtracted	229.072	216.576	12.496
629	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]	Divided	214.256	202.14	1.05994
	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]	Subtracted	229.072	216.576	12.496
630	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	Divided	214.256	202.141	1.05993
631	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]
	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]	Subtracted	229.072	216.576	12.496
632	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	Divided	214.254	202.166	1.05979
633	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	Subtracted	229.072	216.576	12.496
	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]	Divided	234.106	248.104	1.05979
634	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]		226.523	213.786	1.05958
	synapsin i (brain protein 4.1). [swissprot;acc:p17600]	Subtracted	229.072	216.576	12.496
635	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	Divided	228.639	242.258	1.05957
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Subtracted	235.296	247.673	12.377
636	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]	Divided	228.639	242.258	1.05957
	vav proto-oncogene. [swissprot;acc:p15498]	Subtracted	212.2	199.849	12.351
637	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]	Divided	228.639	242.258	1.05957
	vav-3 protein. [swissprot;acc:q9ukw4]	Subtracted	212.253	199.908	12.345
638	sorting nexin 17. [swissprot;acc:q15036]	Divided	228.639	242.258	1.05957
	vav-2 protein. [swissprot;acc:p52735]	Subtracted	212.526	200.212	12.314
639	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	Divided	217.67	230.596	1.05938
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	Subtracted	222.554	234.847	12.293
640	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]		244.842	232.577	12.265

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.