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 1212 to 1261 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
606	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	Subtracted	10231.8	9487.34	744.46	
607	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	Subtracted	10231.8	9487.34	744.46	
607	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	Divided	14976.4	13246.6	1.13058	
608	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Subtracted	2234.68	2978.53	743.85	
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]	Divided	4510.61	5098.74	1.13039	
609	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Divided	3886.62	3438.82	1.13022	
609	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Subtracted	2234.73	2978.57	743.84	
610	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Subtracted	2236.61	2980.35	743.74	
610	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	Divided	8430.03	9518.11	1.12907	
611	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	Divided	5148.71	5811.74	1.12878	
611	fibulin-2 precursor. [source:swissprot;acc:p98095]	Subtracted	8670.59	9412.9	742.31	
612	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Subtracted	5480.24	6222.04	741.8	
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]	Divided	3975.77	4485.05	1.1281	
613	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	Subtracted	5480.24	6222.04	741.8	
613	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Divided	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]	Divided	11222.2	9948.93	1.12798	
614	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	Subtracted	5480.24	6222.04	741.8	
615	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	Subtracted	5480.24	6222.04	741.8	
615	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	Divided	11222.2	9948.93	1.12798	
616	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	Divided	11222.2	9948.93	1.12798	
616	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	Subtracted	5480.24	6222.04	741.8	
617	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Divided	5162.52	5822.47	1.12783	
617	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Subtracted	4532.73	5269.33	736.6	
618	dna mismatch repair protein mlh3 (mutl protein homolog 3). [source:swissprot;acc:q9uhc1]	Subtracted	6327.86	7064.13	736.27	
618	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Divided	7878.27	8879.08	1.12703	
619	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	Divided	3879.99	4371.24	1.12661	
619	ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	Subtracted	6811.2	7547.35	736.15	
620	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [source:refseq;acc:nm_005763]	Subtracted	6807.78	7543.28	735.5	
620	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	Divided	6227.87	7012.9	1.12605	
621	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Divided	4115.39	4633.96	1.12601	
621	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	Subtracted	6805.86	7540.99	735.13	
622	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	Divided	6228.42	7013.21	1.126	
622	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	Subtracted	6805.45	7540.5	735.05	
623	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	Divided	6228.39	7013.19	1.126	
623	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	Subtracted	4490.28	5222.25	731.97	
624	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	Subtracted	4490.28	5222.25	731.97	
624	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	Divided	6228.39	7013.19	1.126	
625	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	Divided	6228.39	7013.19	1.126	
625	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Subtracted	5291.92	6020.19	728.27	
626	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	Divided	6228.39	7013.19	1.126	
626	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	Subtracted	8618.32	9340.98	722.66	
627	limkain b1. [source:refseq;acc:nm_019081]	Divided	6228.39	7013.19	1.126	
627	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [source:swissprot;acc:o60315]	Subtracted	8618.32	9340.98	722.66	
628	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	Divided	6228.39	7013.19	1.126	
628	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [source:swissprot;acc:p37275]	Subtracted	8618.32	9340.98	722.66	
629	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	Divided	6228.39	7013.19	1.126	
629	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Subtracted	5201.41	4479.76	721.65	
630	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Subtracted	5201.41	4479.76	721.65	
630	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	Divided	6228.39	7013.19	1.126	
631	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Subtracted	5201.41	4479.76	721.65	

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/