Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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
Results: HTML CSV LaTeX Showing element 612 to 661 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
612	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	247.47	233.441	1.0601	
613	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	247.47	233.441	1.0601	
614	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	214.257	202.125	1.06002	
615	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	214.257	202.132	1.05999	
616	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	214.257	202.132	1.05999	
617	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	214.257	202.135	1.05997	
618	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	214.256	202.139	1.05994	
619	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	214.256	202.139	1.05994	
620	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	214.256	202.14	1.05994	
621	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	214.256	202.14	1.05994	
622	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	214.256	202.14	1.05994	
623	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	214.256	202.14	1.05994	
624	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	214.256	202.139	1.05994	
625	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	214.256	202.14	1.05994	
626	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	214.256	202.14	1.05994	
627	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	214.256	202.139	1.05994	
628	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	214.256	202.14	1.05994	
629	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	214.256	202.14	1.05994	
630	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	214.256	202.141	1.05993	
631	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	214.256	202.141	1.05993	
632	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	214.254	202.166	1.05979	
633	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]	234.106	248.104	1.05979	
634	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	226.523	213.786	1.05958	
635	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	228.639	242.258	1.05957	
636	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	228.639	242.258	1.05957	
637	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]	228.639	242.258	1.05957	
638	sorting nexin 17. [source:swissprot;acc:q15036]	228.639	242.258	1.05957	
639	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [source:swissprot;acc:p52594]	217.67	230.596	1.05938	
640	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	217.67	230.596	1.05938	
641	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [source:refseq;acc:nm_032152]	217.67	230.596	1.05938	
642	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]	217.67	230.596	1.05938	
643	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [source:refseq;acc:nm_006076]	217.67	230.596	1.05938	
644	cgthba protein (-14 gene protein). [source:swissprot;acc:q12980]	217.67	230.596	1.05938	
645	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [source:refseq;acc:nm_014500]	217.67	230.596	1.05938	
646	short coiled-coil protein; short coiled coil protein. [source:refseq;acc:nm_032547]	216.731	229.549	1.05914	
647	dynein light chain 2. [source:refseq;acc:nm_080677]	216.731	229.549	1.05914	
648	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	218.227	206.078	1.05895	
649	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	233.725	220.751	1.05877	
650	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	228.986	216.276	1.05877	
651	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	233.725	220.751	1.05877	
652	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	248.994	235.255	1.0584	
653	dok-like protein. [source:refseq;acc:nm_024872]	216.504	204.622	1.05807	
654	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	216.504	204.622	1.05807	
655	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	216.504	204.622	1.05807	
656	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	216.504	204.622	1.05807	
657	synapsin iii. [source:swissprot;acc:o14994]	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. [source:refseq;acc:nm_032468]	229.072	216.576	1.0577	
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). [source:swissprot;acc:q9y5j3]	229.072	216.576	1.0577	
660	actin binding lim protein 2. [source:refseq;acc:nm_032432]	229.072	216.576	1.0577	
661	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	229.072	216.576	1.0577	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/