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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Value Type Interaction Map description Network Comparison Type Rank Gene red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2575 to 2624 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	1378	6079.45	6555.4	1.07829	
similar to actin-related protein 3-beta. [source:sptrembl;acc:q96bt2]	1780	5386.37	5744.89	1.06656	
similar to cg5057 gene product. [source:sptrembl;acc:q9btt4]	2984	0.00001	0.00001	1	
similar to cg7020 gene product (fragment). [source:sptrembl;acc:q96ib4]	2316	6960.74	7273.48	1.04493	
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_145245]	1234	5807.83	6300.47	1.08482	
similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	590	6739.85	7644.63	1.13424	
similar to expressed sequence ai415388 (fragment). [source:sptrembl;acc:q8n428]	2098	6024.47	6356.56	1.05512	
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [source:sptrembl;acc:q96ek6]	2066	5882.61	6213.34	1.05622	
similar to kinase suppressor of ras (fragment). [source:sptrembl;acc:q8ivt5]	1429	5880.37	6334.71	1.07726	
similar to lim domain only 7 (fragment). [source:sptrembl;acc:q8n6m2]	1042	5887.52	6434.32	1.09287	
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	3032	0.00001	0.00001	1	
similar to mob-lak. [source:refseq;acc:nm_145279]	2937	0.00001	0.00001	1	
similar to nuclear protein e3-3 orf1. [source:sptrembl;acc:q9bu61]	2710	5603.24	5583.64	1.00351	
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [source:refseq;acc:nm_033557]	1130	5790.65	6303.92	1.08864	
similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	2262	5148.88	5386.34	1.04612	
similar to trna synthetase class ii. [source:refseq;acc:nm_152268]	1195	5439.56	5911.24	1.08671	
similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	1624	4102.1	4392.15	1.07071	
sin3 associated polypeptide p18 (2hor0202). [source:swissprot;acc:o00422]	2518	6204.15	6360.27	1.02516	
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [source:refseq;acc:nm_003864]	2674	7780.98	7741.14	1.00515	
single-minded homolog 1. [source:swissprot;acc:p81133]	1008	5707.73	6249.1	1.09485	
sipl protein. [source:refseq;acc:nm_018269]	910	6522.94	7175.18	1.09999	
sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [source:refseq;acc:nm_012238]	2199	6344.31	6657.98	1.04944	
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]	1244	4835.55	5243.23	1.08431	
skd1 protein (vacuolar sorting protein 4b). [source:swissprot;acc:o75351]	3037	0.00001	0.00001	1	
skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [source:refseq;acc:nm_016532]	2994	0.00001	0.00001	1	
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [source:swissprot;acc:q13643]	2443	3634.59	3756.67	1.03359	
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [source:swissprot;acc:q14192]	2445	3633.14	3754.96	1.03353	
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [source:swissprot;acc:q9nzq9]	1046	4757.46	5198.91	1.09279	
small edrk-rich factor 2. [source:refseq;acc:nm_005770]	2947	0.00001	0.00001	1	
small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	512	10807.4	12338.5	1.14167	
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [source:swissprot;acc:o43765]	565	10434.4	11846.2	1.1353	
small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	705	6912.09	7734.41	1.11897	
small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [source:swissprot;acc:p14648]	3004	0.00001	0.00001	1	
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [source:swissprot;acc:p14678]	3012	0.00001	0.00001	1	
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	204	4512.19	5655.52	1.25339	
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	205	4512.19	5655.52	1.25339	
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	82	4172.91	5954.48	1.42694	
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	141	4405.4	5782.08	1.3125	
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	187	4569.48	5885.79	1.28807	
small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632]	2172	5825.61	6126.74	1.05169	
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	2378	3977.76	3818.09	1.04182	
snare associated protein snapin. [source:refseq;acc:nm_012437]	1198	5721.19	6217.2	1.0867	
snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [source:swissprot;acc:q92966]	2849	0.00001	0.00001	1	
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [source:swissprot;acc:q9y289]	1167	6607.68	7186.45	1.08759	
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [source:swissprot;acc:q92911]	1164	6600.36	7178.84	1.08764	
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [source:swissprot;acc:p05023]	2236	5902.27	6181.21	1.04726	
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	2240	5902.27	6181.21	1.04726	
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [source:swissprot;acc:p13637]	2239	5902.27	6181.21	1.04726	
soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	1475	5910.06	6355.08	1.0753	
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [source:swissprot;acc:q9bzw2]	1078	6439.63	7032.19	1.09202	

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/