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 1093 to 1142 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1093	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [source:swissprot;acc:p43155]	5791.05	6316.61	1.09075	
1094	polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [source:swissprot;acc:q13310]	5791.05	6316.61	1.09075	
1095	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [source:swissprot;acc:p11940]	5791.05	6316.61	1.09075	
1096	kinesin protein. [source:refseq;acc:nm_032559]	5356.23	5842.15	1.09072	
1097	homolog of yeast maf1. [source:refseq;acc:nm_032272]	6133.83	6690.18	1.0907	
1098	tumor differentially expressed protein 2. [source:refseq;acc:nm_178865]	6133.83	6690.18	1.0907	
1099	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [source:swissprot;acc:q13530]	6133.83	6690.18	1.0907	
1100	tumor differentially expressed 1 protein like. [source:swissprot;acc:q9nrx5]	6133.83	6690.18	1.0907	
1101	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [source:swissprot;acc:o43175]	6133.83	6690.18	1.0907	
1102	phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [source:swissprot;acc:q9nsd9]	5462.88	5958.12	1.09066	
1103	ny-ren-62 antigen (fragment). [source:sptrembl;acc:q9y590]	5358.18	5843.73	1.09062	
1104	kinesin-like protein kif2 (kinesin-2) (hk2). [source:swissprot;acc:o00139]	5359.72	5844.97	1.09054	
1105	synaptotagmin xii (sytxii). [source:swissprot;acc:q8iv01]	5460.49	5954.62	1.09049	
1106	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [source:swissprot;acc:q9uj68]	5489.99	5986.63	1.09046	
1107	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [source:swissprot;acc:q9y617]	5489.99	5986.63	1.09046	
1108	rrp5 protein homolog (programmed cell death protein 11). [source:swissprot;acc:q14690]	4846.16	5283.08	1.09016	
1109	rab3a interacting protein (rabin3)-like 1. [source:refseq;acc:nm_013401]	6545.19	7132.89	1.08979	
1110	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [source:swissprot;acc:p22570]	5947.53	6481.56	1.08979	
1111	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [source:refseq;acc:nm_022456]	6540.61	7127.41	1.08972	
1112	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	5910.54	6440.58	1.08968	
1113	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	5910.54	6440.58	1.08968	
1114	phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [source:swissprot;acc:p15259]	5910.54	6440.58	1.08968	
1115	5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	5795.13	6314.19	1.08957	
1116	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [source:swissprot;acc:q13561]	5322.16	5798.38	1.08948	
1117	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	5322.16	5798.38	1.08948	
1118	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [source:swissprot;acc:p12235]	5322.16	5798.38	1.08948	
1119	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [source:swissprot;acc:p05141]	5322.16	5798.38	1.08948	
1120	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	5915.42	6443.77	1.08932	
1121	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [source:swissprot;acc:q9y2x3]	4338.49	4725.86	1.08929	
1122	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [source:swissprot;acc:p48735]	7937.72	8646.38	1.08928	
1123	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	5857.48	6380.4	1.08927	
1124	transducin-like enhancer protein 2 (esg2). [source:swissprot;acc:q04725]	6288.27	6846.97	1.08885	
1125	transducin-like enhancer protein 1 (esg1). [source:swissprot;acc:q04724]	6287.07	6845.28	1.08879	
1126	importin alpha-6 subunit (karyopherin alpha-5 subunit). [source:swissprot;acc:o15131]	5792.08	6305.67	1.08867	
1127	yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [source:refseq;acc:nm_020470]	5790.65	6303.92	1.08864	
1128	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [source:swissprot;acc:o43448]	5790.65	6303.94	1.08864	
1129	voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [source:swissprot;acc:q14722]	5790.65	6303.92	1.08864	
1130	similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [source:refseq;acc:nm_033557]	5790.65	6303.92	1.08864	
1131	aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [source:swissprot;acc:o95154]	5790.65	6303.92	1.08864	
1132	alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [source:refseq;acc:nm_138340]	5790.65	6303.92	1.08864	
1133	golgi membrane protein sb140; smooth muscle cell associated protein 5. [source:refseq;acc:nm_030799]	5790.65	6303.92	1.08864	
1134	alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [source:refseq;acc:nm_152870]	5790.65	6303.92	1.08864	
1135	methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [source:swissprot;acc:q02252]	5790.67	6303.95	1.08864	
1136	10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [source:swissprot;acc:q04984]	5790.65	6303.92	1.08864	
1137	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [source:refseq;acc:nm_006423]	5790.65	6303.92	1.08864	
1138	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [source:swissprot;acc:q9y3b8]	5790.65	6303.92	1.08864	
1139	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [source:swissprot;acc:p28329]	5790.66	6303.95	1.08864	
1140	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [source:swissprot;acc:q13303]	5790.65	6303.93	1.08864	
1141	aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [source:swissprot;acc:o43488]	5790.65	6303.93	1.08864	
1142	importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [source:swissprot;acc:p52294]	5789.07	6302.01	1.0886	

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/