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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank	Gene	description	Network Comparison Type	Value Type	Interaction Map	red	network_comparison	Filtered	green

Results: HTML CSV LaTeX

Showing element 1275 to 1324 of 6456 in total

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

Rank	description	Network Comparison Type	red	network_comparison	green
638	sorting nexin 17. [swissprot;acc:q15036]	Divided	228.639	1.05957	242.258
	vav-2 protein. [swissprot;acc:p52735]	Subtracted	212.526	12.314	200.212
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	1.05938	230.596
	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	12.293	234.847
640	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]		244.842	12.265	232.577
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Divided	217.67	1.05938	230.596
641	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Subtracted	244.842	12.265	232.577
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Divided	217.67	1.05938	230.596
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	12.199	216.745
643	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]	Divided	217.67	1.05938	230.596
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Subtracted	218.227	12.149	206.078
644	cgthba protein (-14 gene protein). [swissprot;acc:q12980]	Divided	217.67	1.05938	230.596
	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	12.142	214.355
645	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]	Divided	217.67	1.05938	230.596
	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Subtracted	226.497	12.142	214.355
646	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	Divided	216.731	1.05914	229.549
	single-minded homolog 1. [swissprot;acc:p81133]	Subtracted	226.497	12.142	214.355
647	dynein light chain 2. [refseq;acc:nm_080677]	Divided	216.731	1.05914	229.549
	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	Subtracted	214.257	12.132	202.125
648	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]			12.125	202.132
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Divided	218.227	1.05895	206.078
649	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]		233.725	1.05877	220.751
	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	Subtracted	214.257	12.125	202.132
650	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]			12.122	202.135
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Divided	228.986	1.05877	216.276
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	12.117	202.139
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	1.0584	235.255
653	dok-like protein. [refseq;acc:nm_024872]		216.504	1.05807	204.622
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Subtracted	214.256	12.117	202.139
654	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Divided	216.504	1.05807	204.622
	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	Subtracted	214.256	12.117	202.139
655	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Divided	216.504	1.05807	204.622
	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	Subtracted	214.256	12.116	202.14
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	1.05807	204.622
657	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]	Subtracted	214.256	12.116	202.14
	synapsin iii. [swissprot;acc:o14994]	Divided	229.072	1.0577	216.576
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	12.116	202.14
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	1.0577	216.576
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	12.116	202.14
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	1.0577	216.576
662	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]	Subtracted	214.256	12.116	202.14
	synapsin ii. [swissprot;acc:q92777]	Divided	229.072	1.0577	216.576

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.