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 red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2075 to 2124 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1038	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]	Divided	186.741	181.041	1.03148	
1038	elks protein. [source:refseq;acc:nm_015064]	Subtracted	218.162	211.648	6.514	
1039	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [source:swissprot;acc:p09622]	Divided	207.719	214.236	1.03137	
1039	phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	Subtracted	220.118	213.685	6.433	
1040	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [source:swissprot;acc:p18405]	Subtracted	220.118	213.685	6.433	
1040	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [source:swissprot;acc:p48643]	Divided	163.24	168.359	1.03136	
1041	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [source:swissprot;acc:p31213]	Subtracted	220.118	213.685	6.433	
1041	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	Divided	186.774	181.099	1.03134	
1042	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	Divided	186.799	181.127	1.03132	
1042	ww domain binding protein 2 (wbp-2). [source:swissprot;acc:q969t9]	Subtracted	216.901	210.485	6.416	
1043	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]	Divided	187.834	182.137	1.03128	
1043	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [source:swissprot;acc:q9y2x3]	Subtracted	239.219	232.837	6.382	
1044	activator of camp-responsive element modulator (crem) in testis; lim protein act. [source:refseq;acc:nm_020482]	Subtracted	269.157	275.531	6.374	
1044	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	Divided	173.475	178.889	1.03121	
1045	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Subtracted	205.632	199.266	6.366	
1045	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	Divided	115.817	119.432	1.03121	
1046	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	Divided	173.475	178.889	1.03121	
1046	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	Subtracted	205.632	199.266	6.366	
1047	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	Divided	187.022	181.391	1.03104	
1047	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	Subtracted	205.632	199.266	6.366	
1048	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Divided	187.96	182.308	1.031	
1048	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	Subtracted	205.632	199.266	6.366	
1049	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	Divided	211.449	217.998	1.03097	
1049	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	Subtracted	205.632	199.266	6.366	
1050	bystin. [source:swissprot;acc:q13895]	Subtracted	239.505	233.185	6.32	
1050	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [source:swissprot;acc:p14061]	Divided	211.449	217.998	1.03097	
1051	17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	Divided	211.449	217.998	1.03097	
1051	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [source:swissprot;acc:p50995]	Subtracted	219.673	213.378	6.295	
1052	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [source:swissprot;acc:q15046]	Subtracted	220.291	226.584	6.293	
1052	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [source:refseq;acc:nm_015725]	Divided	211.449	217.998	1.03097	
1053	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	Subtracted	219.655	213.385	6.27	
1053	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [source:swissprot;acc:p28066]	Divided	207.04	200.84	1.03087	
1054	60s ribosomal protein l21. [source:swissprot;acc:p46778]	Divided	223.958	217.263	1.03082	
1054	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [source:swissprot;acc:p28066]	Subtracted	207.04	200.84	6.2	
1055	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	Divided	219.01	212.468	1.03079	
1055	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Subtracted	138.705	132.538	6.167	
1056	methyltransferase like 2. [source:refseq;acc:nm_018396]	Subtracted	147.211	153.371	6.16	
1056	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [source:swissprot;acc:p38606]	Divided	219.01	212.468	1.03079	
1057	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	Divided	219.01	212.468	1.03079	
1057	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Subtracted	147.211	153.371	6.16	
1058	ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	Divided	228.105	221.293	1.03078	
1058	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Subtracted	147.211	153.371	6.16	
1059	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Divided	228.105	221.293	1.03078	
1059	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Subtracted	147.211	153.371	6.16	
1060	nemo-like kinase; likely ortholog of mouse nemo like kinase. [source:refseq;acc:nm_016231]	Divided	218.162	211.648	1.03078	
1060	septin 6. [source:swissprot;acc:q14141]	Subtracted	126.604	120.463	6.141	
1061	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [source:swissprot;acc:q9y2t2]	Subtracted	217.323	211.185	6.138	
1061	elks protein. [source:refseq;acc:nm_015064]	Divided	218.162	211.648	1.03078	
1062	brain protein 44. [source:swissprot;acc:o95563]	Subtracted	126.215	120.078	6.137	
1062	zinc finger protein 174 (aw-1). [source:swissprot;acc:q15697]	Divided	269.963	278.239	1.03066	

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/