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 568 to 617 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
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	
599	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	3946.32	4475.47	1.13409	
600	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	3946.32	4475.47	1.13409	
601	symplekin. [source:swissprot;acc:q92797]	15213.4	13418.1	1.1338	
602	ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	4864.66	5514.87	1.13366	
603	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	4864.66	5514.87	1.13366	
604	vinculin (metavinculin). [source:swissprot;acc:p18206]	5958.23	6743.37	1.13177	
605	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	6143.52	6950.75	1.1314	
606	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [source:swissprot;acc:p98194]	6148.94	6955.76	1.13121	
607	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	14976.4	13246.6	1.13058	
608	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	4510.61	5098.74	1.13039	
609	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	3886.62	3438.82	1.13022	
610	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	8430.03	9518.11	1.12907	
611	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	5148.71	5811.74	1.12878	
612	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	3975.77	4485.05	1.1281	
613	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	3975.77	4485.05	1.1281	
614	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [source:refseq;acc:nm_018158]	11222.2	9948.93	1.12798	
615	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	11222.2	9948.93	1.12798	
616	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	11222.2	9948.93	1.12798	
617	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	5162.52	5822.47	1.12783	

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/