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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 601 to 650 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
601	VPS39	vam6/vps39-like protein (hvam6p). [source:swissprot;acc:q96jc1]	206.274	218.792	1.06069	
602	MAP4	microtubule-associated protein 4 (map 4). [source:swissprot;acc:p27816]	206.274	218.792	1.06069	
603	LEF1	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	225.829	212.945	1.0605	
604	RPL15	60s ribosomal protein l15. [source:swissprot;acc:p39030]	217.862	230.978	1.0602	
605	HIST1H2BL	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	247.47	233.441	1.0601	
606	HIST2H2BA	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	247.47	233.441	1.0601	
607		histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	247.47	233.441	1.0601	
608		histone h2b. [source:refseq;acc:nm_175055]	247.47	233.441	1.0601	
609		histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	247.47	233.441	1.0601	
610		histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	247.47	233.441	1.0601	
611	HIST3H3	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	247.47	233.441	1.0601	
612	HIST1H2BA	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	HOXA10	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	214.257	202.125	1.06002	
615	HOXB9	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	214.257	202.132	1.05999	
616	HOXA9	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	214.257	202.132	1.05999	
617	HOXC9	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	214.257	202.135	1.05997	
618	GABRG3	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	214.256	202.139	1.05994	
619	FOXG1	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	214.256	202.139	1.05994	
620	GABRG1	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	214.256	202.14	1.05994	
621	GABRA2	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	214.256	202.14	1.05994	
622	GABRA6	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	214.256	202.14	1.05994	
623	GABRG2	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	GABRA4	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	214.256	202.14	1.05994	
626	GABRE	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	214.256	202.14	1.05994	
627	JMJD6	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	214.256	202.139	1.05994	
628	GABRA1	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	214.256	202.14	1.05994	
629	GABRA3	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	214.256	202.14	1.05994	
630	NDUFA6	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	PDXDC1	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	214.256	202.141	1.05993	
632	HOXD9	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	214.254	202.166	1.05979	
633	AARS	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	RPL37	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	228.639	242.258	1.05957	
636	SFRS1	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	PPAT	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]	228.639	242.258	1.05957	
638	SNX17	sorting nexin 17. [source:swissprot;acc:q15036]	228.639	242.258	1.05957	
639	HRB	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	PRAM1	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	HRBL	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	C16orf35	cgthba protein (-14 gene protein). [source:swissprot;acc:q12980]	217.67	230.596	1.05938	
645	HTATSF1	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	SCOC	short coiled-coil protein; short coiled coil protein. [source:refseq;acc:nm_032547]	216.731	229.549	1.05914	
647	DYNLL2	dynein light chain 2. [source:refseq;acc:nm_080677]	216.731	229.549	1.05914	
648	MARS	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	218.227	206.078	1.05895	
649	EIF4E	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	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/