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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 4608 to 4657 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
2304	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	Subtracted	5514.85	5755.17	240.32	
2305	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	Divided	6946.82	7263.87	1.04564	
2305	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	Subtracted	5514.83	5755.14	240.31	
2306	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	Divided	3619.07	3461.21	1.04561	
2306	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [source:swissprot;acc:p42224]	Subtracted	5514.81	5755.1	240.29	
2307	fas apoptotic inhibitory molecule. [source:refseq;acc:nm_018147]	Divided	5666.91	5923.48	1.04528	
2307	germ cell-less. [source:refseq;acc:nm_022471]	Subtracted	7764.92	8003.67	238.75	
2308	60s ribosomal protein l7. [source:swissprot;acc:p18124]	Divided	3976.92	3804.85	1.04522	
2308	pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [source:swissprot;acc:p40424]	Subtracted	7765.3	8004	238.7	
2309	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [source:swissprot;acc:o76062]	Divided	6960.96	7273.7	1.04493	
2309	pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [source:swissprot;acc:p40426]	Subtracted	7765.3	8004	238.7	
2310	hyporthetical protein mgc27169. [source:refseq;acc:nm_176782]	Subtracted	7765.3	8004	238.7	
2310	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [source:swissprot;acc:q14739]	Divided	6960.96	7273.7	1.04493	
2311	homeobox protein meis1. [source:swissprot;acc:o00470]	Subtracted	7765.3	8004	238.7	
2311	solute carrier family 27 member 3; fatty acid transport protein 3. [source:refseq;acc:nm_024330]	Divided	6961.19	7273.93	1.04493	
2312	homeobox protein meis2 (meis1-related protein 1). [source:swissprot;acc:o14770]	Subtracted	7765.3	8004	238.7	
2312	very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [source:swissprot;acc:o14975]	Divided	6960.26	7273.01	1.04493	
2313	bag-family molecular chaperone regulator-2. [source:swissprot;acc:o95816]	Subtracted	7765.3	8004	238.7	
2313	disrupter of silencing 10. [source:refseq;acc:nm_020368]	Divided	6960.96	7273.7	1.04493	
2314	pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [source:swissprot;acc:p40425]	Subtracted	7765.3	8004	238.7	
2314	very long-chain acyl-coa synthetase homolog 1. [source:refseq;acc:nm_014031]	Divided	6960.99	7273.72	1.04493	
2315	pre-b-cell leukemia transcription factor 4. [source:refseq;acc:nm_025245]	Subtracted	7765.3	8004	238.7	
2315	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [source:refseq;acc:nm_012254]	Divided	6961.11	7273.85	1.04493	
2316	homeobox protein meis3 (meis1-related protein 2) (fragment). [source:swissprot;acc:q99687]	Subtracted	7765.3	8004	238.7	
2316	similar to cg7020 gene product (fragment). [source:sptrembl;acc:q96ib4]	Divided	6960.74	7273.48	1.04493	
2317	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	Subtracted	5150.31	5388.05	237.74	
2317	solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [source:refseq;acc:nm_005094]	Divided	6961.44	7274.17	1.04492	
2318	block 23. [source:sptrembl;acc:q8nhw5]	Subtracted	5150.14	5387.84	237.7	
2318	ubiquitin. [source:swissprot;acc:p02248]	Divided	7484.98	7821.11	1.04491	
2319	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [source:swissprot;acc:q9ujm8]	Subtracted	4561.75	4799.24	237.49	
2319	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	Divided	6362.48	6647.42	1.04478	
2320	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	Subtracted	5148.88	5386.34	237.46	
2320	t54 protein. [source:swissprot;acc:q92917]	Divided	6362.48	6647.42	1.04478	
2321	dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [source:swissprot;acc:q9nrf9]	Divided	3496.21	3652.28	1.04464	
2321	wd repeat domain 26. [source:refseq;acc:nm_025160]	Subtracted	6423.46	6655.9	232.44	
2322	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [source:refseq;acc:nm_012301]	Subtracted	5262.6	5492.58	229.98	
2322	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [source:swissprot;acc:q15796]	Divided	6773.67	7075.51	1.04456	
2323	mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [source:swissprot;acc:q15797]	Divided	6773.67	7075.51	1.04456	
2323	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	Subtracted	6123.47	6351.84	228.37	
2324	cop9 subunit 6 (mov34 homolog, 34 kd). [source:refseq;acc:nm_006833]	Divided	6773.67	7075.51	1.04456	
2324	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Subtracted	5123.89	5350.78	226.89	
2325	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [source:swissprot;acc:q15005]	Subtracted	5123.89	5350.78	226.89	
2325	mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [source:swissprot;acc:q92940]	Divided	6773.67	7075.51	1.04456	
2326	histone deacetylase 11 (hd11). [source:swissprot;acc:q96db2]	Divided	6773.67	7075.51	1.04456	
2326	uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [source:swissprot;acc:p11172]	Subtracted	5123.89	5350.78	226.89	
2327	cleft lip and palate associated transmembrane protein 1. [source:refseq;acc:nm_001294]	Subtracted	5123.89	5350.78	226.89	
2327	ethanolamine kinase-like protein eki2 (flj10761). [source:swissprot;acc:q9nvf9]	Divided	6773.67	7075.51	1.04456	
2328	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [source:swissprot;acc:p17213]	Subtracted	5123.89	5350.78	226.89	
2328	ethanolamine kinase (ec 2.7.1.82) (eki). [source:swissprot;acc:q9hbu6]	Divided	6773.67	7075.51	1.04456	
2329	hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [source:refseq;acc:nm_020232]	Divided	6773.67	7075.51	1.04456	

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/