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 1051 to 1100 of 3730 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
549	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	5865.79	6671.23	1.13731	
550	prohibitin. [source:swissprot;acc:p35232]	5773.45	6563.69	1.13687	
551	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	5773.45	6563.69	1.13687	
552	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	15427.2	13572.8	1.13663	
553	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	3853.64	4379.71	1.13651	
554	pre-mrna cleavage complex ii protein clp1. [source:swissprot;acc:q92989]	14830.5	13050.3	1.13641	
555	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	6167.93	7007.7	1.13615	
556	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	6167.93	7007.7	1.13615	
557	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	6167.93	7007.7	1.13615	
558	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	6167.93	7007.7	1.13615	
559	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	6167.93	7007.7	1.13615	
560	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	5480.24	6222.04	1.13536	
561	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	5480.24	6222.04	1.13536	
562	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	5480.24	6222.04	1.13536	
563	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	5480.24	6222.04	1.13536	
564	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	5480.24	6222.04	1.13536	
565	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [source:swissprot;acc:o43765]	10434.4	11846.2	1.1353	
566	autoantigen ngp-1. [source:swissprot;acc:q13823]	3766.14	4274.79	1.13506	
567	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	10264.9	9043.51	1.13506	
568	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [source:swissprot;acc:q8taa5]	4134.77	4691.24	1.13458	
569	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [source:swissprot;acc:q9hav7]	4134.77	4691.24	1.13458	
570	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [source:refseq;acc:nm_003077]	4134.77	4691.24	1.13458	
571	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [source:refseq;acc:nm_003078]	4134.77	4691.24	1.13458	
572	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	4134.77	4691.24	1.13458	
573	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	6739.43	7644.55	1.1343	
574	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	6739.61	7644.58	1.13428	
575	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	6739.63	7644.59	1.13427	
576	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	6739.7	7644.6	1.13426	
577	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	6739.81	7644.62	1.13425	
578	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	6739.81	7644.62	1.13425	
579	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	6739.82	7644.62	1.13425	
580	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	6739.83	7644.63	1.13425	
581	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	6739.82	7644.63	1.13425	
582	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	6739.82	7644.62	1.13425	
583	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	6739.81	7644.62	1.13425	
584	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	6739.82	7644.63	1.13425	
585	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	6739.82	7644.63	1.13425	
586	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	6739.81	7644.62	1.13425	
587	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	6739.83	7644.63	1.13425	
588	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	6739.83	7644.63	1.13425	
589	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	6739.85	7644.63	1.13424	
590	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	6739.85	7644.63	1.13424	
591	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	6740.5	7644.76	1.13415	
592	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	3946.32	4475.47	1.13409	
593	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	3946.32	4475.47	1.13409	
594	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]	3946.32	4475.47	1.13409	
595	histone h2b. [source:refseq;acc:nm_175055]	3946.32	4475.47	1.13409	
596	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	3946.32	4475.47	1.13409	
597	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	3946.32	4475.47	1.13409	
598	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	3946.32	4475.47	1.13409	

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/