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 1033 to 1082 of 3228 in total

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

Rank	description	red	green	network_comparison	
1033	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	6080.91	6653.52	1.09417	
1034	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [source:swissprot;acc:q00266]	6152.88	6732.12	1.09414	
1035	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [source:swissprot;acc:p48730]	5054.73	5530.23	1.09407	
1036	fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:p09467]	6077.65	6649.22	1.09404	
1037	monoglyceride lipase; lysophospholipase-like. [source:refseq;acc:nm_007283]	6544.26	7159.43	1.094	
1038	myb proto-oncogene protein (c-myb). [source:swissprot;acc:p10242]	5417.95	5924.41	1.09348	
1039	myb-related protein b (b-myb). [source:swissprot;acc:p10244]	5418.92	5923.09	1.09304	
1040	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	5421.93	5926.08	1.09298	
1041	myb-related protein a (a-myb). [source:swissprot;acc:p10243]	5419.18	5922.84	1.09294	
1042	similar to lim domain only 7 (fragment). [source:sptrembl;acc:q8n6m2]	5887.52	6434.32	1.09287	
1043	15 kda selenoprotein precursor. [source:swissprot;acc:o60613]	6344.41	6933.36	1.09283	
1044	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [source:refseq;acc:nm_015517]	4757.46	5198.91	1.09279	
1045	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [source:swissprot;acc:q14197]	5364.32	5862.09	1.09279	
1046	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [source:swissprot;acc:q9nzq9]	4757.46	5198.91	1.09279	
1047	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [source:swissprot;acc:q9nyl9]	4757.46	5198.91	1.09279	
1048	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [source:swissprot;acc:p28289]	4757.46	5198.91	1.09279	
1049	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [source:swissprot;acc:q9y5x1]	4757.46	5198.91	1.09279	
1050	neuronal tropomodulin (n-tmod) (tropomodulin 2). [source:swissprot;acc:q9nzr1]	4757.46	5198.91	1.09279	
1051	homeobox protein dlx-2. [source:swissprot;acc:q07687]	4757.46	5198.91	1.09279	
1052	homeobox protein dlx-5. [source:swissprot;acc:p56178]	4757.46	5198.91	1.09279	
1053	fetal brain protein 239 (239fb). [source:swissprot;acc:q15777]	4757.46	5198.91	1.09279	
1054	homeobox protein dlx-3. [source:swissprot;acc:o60479]	4757.46	5198.91	1.09279	
1055	activated p21cdc42hs kinase. [source:refseq;acc:nm_005781]	4757.46	5198.91	1.09279	
1056	mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [source:refseq;acc:nm_015093]	4757.46	5198.91	1.09279	
1057	tata element modulatory factor (tmf). [source:swissprot;acc:p82094]	5412.23	5913.4	1.0926	
1058	scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [source:refseq;acc:nm_020680]	5412.23	5913.4	1.0926	
1059	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [source:swissprot;acc:q15814]	5719.01	6248.6	1.0926	
1060	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [source:swissprot;acc:q9y305]	5719.01	6248.6	1.0926	
1061	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [source:swissprot;acc:p52948]	5412.23	5913.4	1.0926	
1062	ammecr1 protein. [source:refseq;acc:nm_015365]	5412.23	5913.4	1.0926	
1063	mrna-associated protein mrnp 41 (rae1 protein homolog). [source:swissprot;acc:p78406]	5412.23	5913.4	1.0926	
1064	dead-box protein. [source:refseq;acc:nm_018665]	5719.01	6248.6	1.0926	
1065	dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [source:swissprot;acc:p27695]	6393.81	6984.94	1.09245	
1066	leucyl-trna synthetase. [source:refseq;acc:nm_020117]	5417.06	5917.79	1.09244	
1067	probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [source:swissprot;acc:q15031]	5417.07	5917.79	1.09243	
1068	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	6201.54	6774.35	1.09237	
1069	elongation factor 2 (ef-2). [source:swissprot;acc:p13639]	5494.73	6001.08	1.09215	
1070	metabotropic glutamate receptor 2 precursor (mglur2). [source:swissprot;acc:q14416]	5494.73	6001.08	1.09215	
1071	metabotropic glutamate receptor 3 precursor (mglur3). [source:swissprot;acc:q14832]	5494.73	6001.08	1.09215	
1072	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	5207.39	5687.2	1.09214	
1073	prefoldin subunit 2 (hspc231). [source:swissprot;acc:q9uhv9]	5207.39	5687.2	1.09214	
1074	uxt protein (ubiquitously expressed transcript protein) (hspc024). [source:swissprot;acc:q9ubk9]	5207.39	5687.2	1.09214	
1075	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	6441.56	7034.86	1.09211	
1076	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [source:swissprot;acc:q9ukg4]	6439.63	7032.19	1.09202	
1077	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [source:swissprot;acc:q8wwt9]	6439.66	7032.22	1.09202	
1078	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [source:swissprot;acc:q9bzw2]	6439.63	7032.19	1.09202	
1079	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [source:swissprot;acc:q13183]	6439.66	7032.22	1.09202	
1080	secretory carrier-associated membrane protein 2. [source:swissprot;acc:o15127]	6439.3	7031.73	1.092	
1081	secretory carrier-associated membrane protein 3. [source:swissprot;acc:o14828]	6439.3	7031.73	1.092	
1082	secretory carrier-associated membrane protein 1. [source:swissprot;acc:o15126]	6439.35	7031.8	1.092	

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/