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 Rank Network Comparison Type Gene red green Filtered network_comparison

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Showing element 2208 to 2257 of 3228 in total

Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	313	21644.2	18098.7	1.1959	
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [source:refseq;acc:nm_003981]	1887	5438.6	5783.11	1.06335	
protein sck (fragment). [source:swissprot;acc:p98077]	1827	5633.44	5997	1.06454	
protein tara (trio-associated repeat on actin) (hrihfb2122). [source:swissprot;acc:q9h2d6]	2576	5608.22	5712.39	1.01857	
protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	2023	3560.24	3364.84	1.05807	
protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	1988	3559.49	3360.39	1.05925	
protein transport protein sec23a (sec23-related protein a). [source:swissprot;acc:q15436]	3135	0.00001	0.00001	1	
protein transport protein sec23b (sec23-related protein b). [source:swissprot;acc:q15437]	3127	0.00001	0.00001	1	
protein transport protein sec24a (sec24-related protein a) (fragment). [source:swissprot;acc:o95486]	3056	0.00001	0.00001	1	
protein transport protein sec24b (sec24-related protein b). [source:swissprot;acc:o95487]	2956	0.00001	0.00001	1	
protein transport protein sec24c (sec24-related protein c). [source:swissprot;acc:p53992]	2910	0.00001	0.00001	1	
protein transport protein sec24d (sec24-related protein d). [source:swissprot;acc:o94855]	2903	0.00001	0.00001	1	
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	2079	3614.91	3423.89	1.05579	
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	2078	3614.91	3423.89	1.05579	
protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	2265	3612.45	3453.39	1.04606	
protein x 0001. [source:refseq;acc:nm_016302]	1582	6376.12	6833.59	1.07175	
protein x 0004. [source:refseq;acc:nm_016301]	16	2671	871	3.06659	
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	538	10603.5	12069.4	1.13825	
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	1247	6278.76	6807.51	1.08421	
protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [source:swissprot;acc:q06124]	2789	0.00001	0.00001	1	
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [source:swissprot;acc:p17706]	1248	6275.86	6803.95	1.08415	
proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	248	6417.18	7859.6	1.22477	
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	83	4932.27	7033.29	1.42597	
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	253	6417.18	7859.59	1.22477	
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [source:swissprot;acc:p16591]	1649	6079.19	6503.12	1.06973	
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [source:swissprot;acc:p07332]	1645	6079.19	6503.12	1.06973	
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	255	6417.18	7859.6	1.22477	
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	254	6417.18	7859.6	1.22477	
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	250	6417.18	7859.6	1.22477	
protocadherin 15 precursor. [source:swissprot;acc:q96qu1]	1181	4392.63	4776.19	1.08732	
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [source:swissprot;acc:q96jq0]	2838	0.00001	0.00001	1	
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [source:swissprot;acc:q9nyq8]	1722	5458.12	5830.76	1.06827	
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [source:swissprot;acc:q12887]	933	5638.46	6194.04	1.09853	
protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [source:swissprot;acc:p50336]	2934	0.00001	0.00001	1	
prp18 pre-mrna processing factor 18 homolog. [source:refseq;acc:nm_003675]	2707	8979.61	9012.31	1.00364	
ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	364	5189	6088.47	1.17334	
ptd016 protein. [source:refseq;acc:nm_016125]	3093	0.00001	0.00001	1	
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491]	1444	5450.9	5869.07	1.07672	
puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [source:swissprot;acc:p55786]	828	5745.61	6354.75	1.10602	
putatative 28 kda protein. [source:refseq;acc:nm_020143]	2747	4708.68	4702.58	1.0013	
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [source:swissprot;acc:q9y305]	1060	5719.01	6248.6	1.0926	
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	626	6228.39	7013.19	1.126	
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	628	6228.39	7013.19	1.126	
putative ankyrin-repeat containing protein. [source:refseq;acc:nm_025185]	1720	5458.12	5830.76	1.06827	
putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	147	11068	8508.5	1.30082	
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [source:swissprot;acc:o60774]	952	5364.3	5885.48	1.09716	
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	2439	3754.39	3629.51	1.03441	
putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [source:swissprot;acc:o75153]	1193	5464.9	5940.16	1.08697	
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	291	44490.5	36927.5	1.20481	
putative gtp-binding protein ptd004 (pro2455). [source:swissprot;acc:q9ntk5]	2089	5775.22	6094.89	1.05535	

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/