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	green	red	network_comparison

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Showing element 1251 to 1300 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
626	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]	Divided	202.14	214.256	1.05994
	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]	Subtracted	216.576	229.072	12.496
627	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	Divided	202.139	214.256	1.05994
	synapsin ii. [swissprot;acc:q92777]	Subtracted	216.576	229.072	12.496
628	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]	Divided	202.14	214.256	1.05994
	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]	Subtracted	216.576	229.072	12.496
629	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]	Divided	202.14	214.256	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	216.576	229.072	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	202.141	214.256	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	216.576	229.072	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	202.166	214.254	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	216.576	229.072	12.496
	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]	Divided	248.104	234.106	1.05979
634	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]		213.786	226.523	1.05958
	synapsin i (brain protein 4.1). [swissprot;acc:p17600]	Subtracted	216.576	229.072	12.496
635	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	Divided	242.258	228.639	1.05957
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Subtracted	247.673	235.296	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	242.258	228.639	1.05957
	vav proto-oncogene. [swissprot;acc:p15498]	Subtracted	199.849	212.2	12.351
637	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]	Divided	242.258	228.639	1.05957
	vav-3 protein. [swissprot;acc:q9ukw4]	Subtracted	199.908	212.253	12.345
638	sorting nexin 17. [swissprot;acc:q15036]	Divided	242.258	228.639	1.05957
	vav-2 protein. [swissprot;acc:p52735]	Subtracted	200.212	212.526	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	230.596	217.67	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	234.847	222.554	12.293
640	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]		232.577	244.842	12.265
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Divided	230.596	217.67	1.05938
641	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Subtracted	232.577	244.842	12.265
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Divided	230.596	217.67	1.05938
642	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	Subtracted	216.745	228.944	12.199
643	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]	Divided	230.596	217.67	1.05938
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Subtracted	206.078	218.227	12.149
644	cgthba protein (-14 gene protein). [swissprot;acc:q12980]	Divided	230.596	217.67	1.05938
	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	Subtracted	214.355	226.497	12.142
645	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]	Divided	230.596	217.67	1.05938
	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Subtracted	214.355	226.497	12.142
646	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	Divided	229.549	216.731	1.05914
	single-minded homolog 1. [swissprot;acc:p81133]	Subtracted	214.355	226.497	12.142
647	dynein light chain 2. [refseq;acc:nm_080677]	Divided	229.549	216.731	1.05914
	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	Subtracted	202.125	214.257	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	206.078	218.227	1.05895
649	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]		220.751	233.725	1.05877
	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	Subtracted	202.132	214.257	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	216.276	228.986	1.05877

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.