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 2325 to 2374 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1163	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [source:refseq;acc:nm_052853]	Subtracted	5799.35	6305.95	506.6	
1163	elks protein. [source:refseq;acc:nm_015064]	Divided	5832.13	6343.59	1.0877	
1164	aarf domain containing kinase 4. [source:refseq;acc:nm_024876]	Subtracted	5799.35	6305.95	506.6	
1164	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [source:swissprot;acc:q92911]	Divided	6600.36	7178.84	1.08764	
1165	aarf domain containing kinase 1. [source:refseq;acc:nm_020421]	Subtracted	5799.35	6305.95	506.6	
1165	kidney and liver proline oxidase 1. [source:refseq;acc:nm_021232]	Divided	6604.44	7183.07	1.08761	
1166	exocyst complex component sec8. [source:swissprot;acc:q96a65]	Subtracted	6221.22	6727.77	506.55	
1166	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [source:refseq;acc:nm_145913]	Divided	6606.3	7185.01	1.0876	
1167	myb proto-oncogene protein (c-myb). [source:swissprot;acc:p10242]	Subtracted	5417.95	5924.41	506.46	
1167	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [source:swissprot;acc:q9y289]	Divided	6607.68	7186.45	1.08759	
1168	elongation factor 2 (ef-2). [source:swissprot;acc:p13639]	Subtracted	5494.73	6001.08	506.35	
1168	mitotic checkpoint protein bub3. [source:swissprot;acc:o43684]	Divided	5470.44	5949.49	1.08757	
1169	metabotropic glutamate receptor 2 precursor (mglur2). [source:swissprot;acc:q14416]	Subtracted	5494.73	6001.08	506.35	
1169	zinc finger protein 207. [source:swissprot;acc:o43670]	Divided	5470.44	5949.49	1.08757	
1170	metabotropic glutamate receptor 3 precursor (mglur3). [source:swissprot;acc:q14832]	Subtracted	5494.73	6001.08	506.35	
1170	ubiquitin-like protein smt3a. [source:swissprot;acc:p55854]	Divided	5826.34	6335.98	1.08747	
1171	red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [source:swissprot;acc:p24666]	Subtracted	4986.58	5492.51	505.93	
1171	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Divided	5826.29	6335.93	1.08747	
1172	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	Divided	5826.32	6335.95	1.08747	
1172	branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [source:swissprot;acc:p54687]	Subtracted	5890.62	6396.53	505.91	
1173	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [source:swissprot;acc:o15382]	Subtracted	5892.05	6397.28	505.23	
1173	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [source:swissprot;acc:q8ni60]	Divided	5799.35	6305.95	1.08735	
1174	cda11 protein. [source:refseq;acc:nm_032026]	Divided	5874.11	6387.23	1.08735	
1174	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	Subtracted	4088.63	4593.43	504.8	
1175	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [source:refseq;acc:nm_052853]	Divided	5799.35	6305.95	1.08735	
1175	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	Subtracted	4088.63	4593.43	504.8	
1176	aarf domain containing kinase 4. [source:refseq;acc:nm_024876]	Divided	5799.35	6305.95	1.08735	
1176	myb-related protein b (b-myb). [source:swissprot;acc:p10244]	Subtracted	5418.92	5923.09	504.17	
1177	aarf domain containing kinase 1. [source:refseq;acc:nm_020421]	Divided	5799.35	6305.95	1.08735	
1177	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	Subtracted	5421.93	5926.08	504.15	
1178	myb-related protein a (a-myb). [source:swissprot;acc:p10243]	Subtracted	5419.18	5922.84	503.66	
1178	pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	Divided	4392.63	4776.19	1.08732	
1179	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	Subtracted	4019.88	4522.61	502.73	
1179	solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [source:refseq;acc:nm_006749]	Divided	4392.63	4776.19	1.08732	
1180	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [source:swissprot;acc:p14324]	Divided	4392.63	4776.19	1.08732	
1180	tata element modulatory factor (tmf). [source:swissprot;acc:p82094]	Subtracted	5412.23	5913.4	501.17	
1181	protocadherin 15 precursor. [source:swissprot;acc:q96qu1]	Divided	4392.63	4776.19	1.08732	
1181	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]	Subtracted	5412.23	5913.4	501.17	
1182	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [source:swissprot;acc:p52948]	Subtracted	5412.23	5913.4	501.17	
1182	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [source:refseq;acc:nm_005415]	Divided	4392.63	4776.19	1.08732	
1183	ammecr1 protein. [source:refseq;acc:nm_015365]	Subtracted	5412.23	5913.4	501.17	
1183	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	Divided	4392.63	4776.19	1.08732	
1184	mrna-associated protein mrnp 41 (rae1 protein homolog). [source:swissprot;acc:p78406]	Subtracted	5412.23	5913.4	501.17	
1184	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [source:swissprot;acc:p08151]	Divided	4392.63	4776.19	1.08732	
1185	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [source:swissprot;acc:o75381]	Subtracted	6522.96	7023.77	500.81	
1185	suppressor of fused. [source:refseq;acc:nm_016169]	Divided	4392.63	4776.19	1.08732	
1186	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	Subtracted	6222.8	6723.54	500.74	
1186	zinc finger protein gli3. [source:swissprot;acc:p10071]	Divided	4392.63	4776.19	1.08732	
1187	leucyl-trna synthetase. [source:refseq;acc:nm_020117]	Subtracted	5417.06	5917.79	500.73	
1187	limb region 1 protein; limb region 1. [source:refseq;acc:nm_022458]	Divided	4392.63	4776.19	1.08732	

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/