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 1275 to 1324 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
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
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Divided	217.67	230.596	1.05938
641	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Subtracted	244.842	232.577	12.265
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Divided	217.67	230.596	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	228.944	216.745	12.199
643	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]	Divided	217.67	230.596	1.05938
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Subtracted	218.227	206.078	12.149
644	cgthba protein (-14 gene protein). [swissprot;acc:q12980]	Divided	217.67	230.596	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	226.497	214.355	12.142
645	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]	Divided	217.67	230.596	1.05938
	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Subtracted	226.497	214.355	12.142
646	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	Divided	216.731	229.549	1.05914
	single-minded homolog 1. [swissprot;acc:p81133]	Subtracted	226.497	214.355	12.142
647	dynein light chain 2. [refseq;acc:nm_080677]	Divided	216.731	229.549	1.05914
	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

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.