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 1051 to 1100 of 7460 in total 
Value Type	Measured
Interaction Map	High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison	
263	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]	Divided	0	1843	1633	1.1286	
263	trs85 homolog. [source:swissprot;acc:q9y2l5]	Divided	1	24896.4	20431.7	1.21852	
264	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]	Subtracted	0	1837.26	1721.76	115.5	
264	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Divided	1	4987.58	4094.57	1.2181	
264	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	Subtracted	1	12503.3	11212	1291.3	
264	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	Divided	0	3336.48	2957.12	1.12829	
265	60s ribosomal protein l9. [source:swissprot;acc:p32969]	Divided	0	1685.44	1894.01	1.12375	
265	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Subtracted	0	0	109	109	
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Subtracted	1	4638.1	5923.4	1285.3	
265	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	Divided	1	24806.9	20369.9	1.21782	
266	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Subtracted	0	1212.82	1104.61	108.21	
266	aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	Divided	0	1475.05	1312.91	1.1235	
266	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Divided	1	24806.9	20369.9	1.21782	
266	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]	Subtracted	1	11222.2	9948.93	1273.27	
267	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	Subtracted	1	11222.2	9948.93	1273.27	
267	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Subtracted	0	870.93	975.647	104.717	
267	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Divided	1	14021.4	11523	1.21682	
267	uncharacterized bone marrow protein bm033. [source:refseq;acc:nm_018452]	Divided	0	1475.05	1312.91	1.1235	
268	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	Subtracted	1	11222.2	9948.93	1273.27	
268	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Divided	1	24473.9	20127.8	1.21593	
268	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	Subtracted	0	861.401	759.896	101.505	
268	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [source:refseq;acc:nm_003902]	Divided	0	604.529	538.094	1.12346	
269	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Divided	0	1217.92	1367.83	1.12309	
269	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Subtracted	1	4808.79	6074.21	1265.42	
269	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Subtracted	0	118.878	17.6611	101.217	
269	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Divided	1	4590.18	5575.52	1.21466	
270	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	Divided	1	23640.2	19479.8	1.21358	
270	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	Subtracted	0	157	56	101	
270	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Divided	0	1217.96	1367.88	1.12309	
270	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Subtracted	1	4810.22	6075.04	1264.82	
271	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Subtracted	0	3024.78	2923.92	100.86	
271	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Divided	1	2554.89	3093.78	1.21092	
271	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Subtracted	1	4812.01	6076.09	1264.08	
271	histone h4. [source:swissprot;acc:p02304]	Divided	0	21773.1	24446.3	1.12278	
272	60s ribosomal protein l15. [source:swissprot;acc:p39030]	Divided	0	846.216	753.793	1.12261	
272	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Divided	1	3858.52	4669.27	1.21012	
272	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [source:swissprot;acc:q16543]	Subtracted	0	750.981	650.724	100.257	
272	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Subtracted	1	1991.03	3221.38	1230.35	
273	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	Subtracted	0	658.544	758.411	99.867	
273	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Divided	1	3199.4	3870.8	1.20985	
273	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Subtracted	1	5181.2	6410.58	1229.38	
273	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Divided	0	1410.81	1582.65	1.1218	
274	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	Subtracted	0	1491.75	1591.6	99.85	
274	brain protein 16. [source:refseq;acc:nm_016458]	Divided	0	2155.75	2418.14	1.12172	
274	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	Divided	1	3119.98	2579.49	1.20953	
274	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Subtracted	1	5181.2	6410.58	1229.38	
275	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	Subtracted	1	10264.9	9043.51	1221.39	
275	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [source:refseq;acc:nm_032152]	Subtracted	0	2156.64	2254.12	97.48	
275	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	Divided	1	3119.98	2579.49	1.20953	
275	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [source:refseq;acc:nm_003075]	Divided	0	717.401	804.725	1.12172	

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/