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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 613 to 662 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	green	description	network_comparison	red
613	233.441	histone h2b.e (h2b/e). [swissprot;acc:q99879]	1.0601	247.47
614	202.125	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	1.06002	214.257
615	202.132	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	1.05999
616		homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
617	202.135	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	1.05997
618	202.139	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	1.05994	214.256
619		forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
620	202.14	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]
621		gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
622		gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
623		gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]
624	202.139	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]
625	202.14	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]
626		gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
627	202.139	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]
628	202.14	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]
629		gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
630	202.141	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	1.05993
631		similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]
632	202.166	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	1.05979	214.254
633	248.104	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]		234.106
634	213.786	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	1.05958	226.523
635	242.258	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	1.05957	228.639
636		splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]
637		amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
638		sorting nexin 17. [swissprot;acc:q15036]
639	230.596	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	1.05938	217.67
640		intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
641		pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]
642		intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
643		hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]
644		cgthba protein (-14 gene protein). [swissprot;acc:q12980]
645		hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]
646	229.549	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	1.05914	216.731
647		dynein light chain 2. [refseq;acc:nm_080677]
648	206.078	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	1.05895	218.227
649	220.751	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	1.05877	233.725
650	216.276	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]		228.986
651	220.751	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]		233.725
652	235.255	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	1.0584	248.994
653	204.622	dok-like protein. [refseq;acc:nm_024872]	1.05807	216.504
654		docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]
655		docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
656		tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]
657	216.576	synapsin iii. [swissprot;acc:o14994]	1.0577	229.072
658		aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
659		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]
660		actin binding lim protein 2. [refseq;acc:nm_032432]
661		hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]
662		synapsin ii. [swissprot;acc:q92777]

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.