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 green red network_comparison

Results: HTML CSV LaTeX

Showing element 475 to 524 of 3730 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	green	red	network_comparison	
238	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	0	13941.7	12677.7	1.0997	
238	rd protein. [source:swissprot;acc:p18615]	1	254.15	227.357	1.11785	
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	1	254.15	227.357	1.11785	
239	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	0	9795.36	8907.41	1.09969	
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	1	254.15	227.357	1.11785	
240	methyltransferase like 2. [source:refseq;acc:nm_018396]	0	16326	17946	1.09923	
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	1	254.15	227.357	1.11785	
241	secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	0	12743.3	14003.7	1.09891	
242	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	0	13895.8	15260.6	1.09822	
242	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	1	254.15	227.357	1.11785	
243	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	0	1373	1251	1.09752	
243	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	1	254.15	227.357	1.11785	
244	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	1	254.15	227.357	1.11785	
244	keratin associated protein 9.2. [source:refseq;acc:nm_031961]	0	11579.9	10551.1	1.09751	
245	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	0	13019	11867.6	1.09702	
245	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	1	202.333	226.109	1.11751	
246	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	1	212.363	237.312	1.11748	
246	keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]	0	11573.7	10551.6	1.09687	
247	keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	0	11573.7	10551.6	1.09687	
247	rna-binding protein. [source:refseq;acc:nm_019027]	1	212.41	237.302	1.11719	
248	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	1	212.41	237.302	1.11719	
248	keratin associated protein 1.5. [source:refseq;acc:nm_031957]	0	11573.7	10551.6	1.09687	
249	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	0	11573.7	10551.6	1.09687	
249	ns1-associated protein 1. [source:refseq;acc:nm_006372]	1	212.41	237.302	1.11719	
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	1	212.41	237.302	1.11719	
250	keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm_030966]	0	11573.7	10551.6	1.09687	
251	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	0	11573.6	10551.6	1.09686	
251	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	1	166.661	186.172	1.11707	
252	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	1	212.457	237.292	1.11689	
252	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	0	11573.5	10551.6	1.09685	
253	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	0	11573.5	10551.6	1.09685	
253	mad protein (max dimerizer). [source:swissprot;acc:q05195]	1	204.333	228	1.11583	
254	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	0	11573.5	10551.6	1.09685	
254	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	1	179.88	200.691	1.11569	
255	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	1	179.88	200.691	1.11569	
255	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	0	11573.5	10551.6	1.09685	
256	espin. [source:refseq;acc:nm_031475]	0	11573.4	10551.6	1.09684	
256	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	1	204.357	227.999	1.11569	
257	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	1	179.88	200.691	1.11569	
257	keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	0	11566.4	10552.2	1.09611	
258	40s ribosomal protein s28. [source:swissprot;acc:p25112]	0	14193.6	12967.1	1.09459	
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	1	204.366	227.999	1.11564	
259	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	0	9549.77	10438.3	1.09304	
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	1	204.37	227.999	1.11562	
260	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	0	11392.6	12447.6	1.0926	
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	1	196.978	219.421	1.11394	
261	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	0	11393.9	12448.9	1.09259	
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	1	196.978	219.421	1.11394	
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	1	196.978	219.421	1.11394	
262	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	0	3778	3464	1.09065	

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/