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 2175 to 2224 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1088	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [source:swissprot;acc:q99933]	Subtracted	6439.79	6959.21	519.42	
1088	tax interaction protein 1. [source:refseq;acc:nm_014604]	Divided	5732.73	6256.63	1.09139	
1089	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [source:swissprot;acc:p49840]	Subtracted	6439.79	6959.21	519.42	
1089	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [source:swissprot;acc:p21549]	Divided	6390.28	6973.08	1.0912	
1090	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [source:swissprot;acc:p49841]	Subtracted	6439.79	6959.21	519.42	
1090	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	Divided	5651.07	6164.55	1.09086	
1091	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [source:swissprot;acc:q92871]	Subtracted	5509.89	6029.29	519.4	
1091	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	Divided	5791.05	6316.61	1.09075	
1092	dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [source:swissprot;acc:q01740]	Subtracted	5365.14	5884.43	519.29	
1092	hskin17 protein. [source:refseq;acc:nm_012311]	Divided	5791.05	6316.61	1.09075	
1093	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [source:swissprot;acc:p43155]	Divided	5791.05	6316.61	1.09075	
1093	dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [source:swissprot;acc:p31512]	Subtracted	5365.22	5884.32	519.1	
1094	5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	Subtracted	5795.13	6314.19	519.06	
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]	Divided	5791.05	6316.61	1.09075	
1095	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Subtracted	4115.39	4633.96	518.57	
1095	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [source:swissprot;acc:p11940]	Divided	5791.05	6316.61	1.09075	
1096	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	Subtracted	6334.15	6852.61	518.46	
1096	kinesin protein. [source:refseq;acc:nm_032559]	Divided	5356.23	5842.15	1.09072	
1097	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Subtracted	4708.61	5226.71	518.1	
1097	homolog of yeast maf1. [source:refseq;acc:nm_032272]	Divided	6133.83	6690.18	1.0907	
1098	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	Subtracted	4708.61	5226.71	518.1	
1098	tumor differentially expressed protein 2. [source:refseq;acc:nm_178865]	Divided	6133.83	6690.18	1.0907	
1099	40s ribosomal protein s19. [source:swissprot;acc:p39019]	Subtracted	4708.61	5226.71	518.1	
1099	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [source:swissprot;acc:q13530]	Divided	6133.83	6690.18	1.0907	
1100	60s ribosomal protein l31. [source:swissprot;acc:p12947]	Subtracted	4708.61	5226.71	518.1	
1100	tumor differentially expressed 1 protein like. [source:swissprot;acc:q9nrx5]	Divided	6133.83	6690.18	1.0907	
1101	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [source:swissprot;acc:o43175]	Divided	6133.83	6690.18	1.0907	
1101	exocyst complex component sec10 (hsec10). [source:swissprot;acc:o00471]	Subtracted	6721.25	7238.34	517.09	
1102	phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [source:swissprot;acc:q9nsd9]	Divided	5462.88	5958.12	1.09066	
1102	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [source:swissprot;acc:o15525]	Subtracted	7433.73	7950.61	516.88	
1103	ny-ren-62 antigen (fragment). [source:sptrembl;acc:q9y590]	Divided	5358.18	5843.73	1.09062	
1103	transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [source:swissprot;acc:q9ulx9]	Subtracted	7433.73	7950.61	516.88	
1104	kinesin-like protein kif2 (kinesin-2) (hk2). [source:swissprot;acc:o00139]	Divided	5359.72	5844.97	1.09054	
1104	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [source:swissprot;acc:o60675]	Subtracted	7433.73	7950.61	516.88	
1105	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [source:refseq;acc:nm_006614]	Subtracted	7433.73	7950.61	516.88	
1105	synaptotagmin xii (sytxii). [source:swissprot;acc:q8iv01]	Divided	5460.49	5954.62	1.09049	
1106	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [source:swissprot;acc:p32004]	Subtracted	7433.73	7950.61	516.88	
1106	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [source:swissprot;acc:q9uj68]	Divided	5489.99	5986.63	1.09046	
1107	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [source:swissprot;acc:q9y617]	Divided	5489.99	5986.63	1.09046	
1107	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [source:swissprot;acc:q16594]	Subtracted	7433.73	7950.61	516.88	
1108	nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [source:swissprot;acc:q14494]	Subtracted	7433.73	7950.61	516.88	
1108	rrp5 protein homolog (programmed cell death protein 11). [source:swissprot;acc:q14690]	Divided	4846.16	5283.08	1.09016	
1109	nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [source:refseq;acc:nm_004289]	Subtracted	7433.73	7950.61	516.88	
1109	rab3a interacting protein (rabin3)-like 1. [source:refseq;acc:nm_013401]	Divided	6545.19	7132.89	1.08979	
1110	mstp028 protein. [source:refseq;acc:nm_031954]	Subtracted	5838.87	6355.06	516.19	
1110	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [source:swissprot;acc:p22570]	Divided	5947.53	6481.56	1.08979	
1111	putative sialoglycoprotease type 2. [source:refseq;acc:nm_022353]	Subtracted	5393.37	5909.47	516.1	
1111	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [source:refseq;acc:nm_022456]	Divided	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]	Divided	5910.54	6440.58	1.08968	
1112	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [source:swissprot;acc:q12824]	Subtracted	5840.01	6355.56	515.55	

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/