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 2062 to 2111 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1031	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [source:swissprot;acc:q9nr77]	Subtracted	6437.99	6969.67	531.68	
1032	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [source:swissprot;acc:p54652]	Subtracted	6437.99	6969.67	531.68	
1032	ran binding protein 11. [source:refseq;acc:nm_016338]	Divided	6138.91	6717.05	1.09418	
1033	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	Divided	6080.91	6653.52	1.09417	
1033	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	Subtracted	6437.99	6969.67	531.68	
1034	heat shock cognate 71 kda protein. [source:swissprot;acc:p11142]	Subtracted	6437.99	6969.67	531.68	
1034	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [source:swissprot;acc:q00266]	Divided	6152.88	6732.12	1.09414	
1035	beta-catenin (pro2286). [source:swissprot;acc:p35222]	Subtracted	5635.26	6166.09	530.83	
1035	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [source:swissprot;acc:p48730]	Divided	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]	Divided	6077.65	6649.22	1.09404	
1036	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Subtracted	5910.54	6440.58	530.04	
1037	monoglyceride lipase; lysophospholipase-like. [source:refseq;acc:nm_007283]	Divided	6544.26	7159.43	1.094	
1037	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]	Subtracted	5910.54	6440.58	530.04	
1038	myb proto-oncogene protein (c-myb). [source:swissprot;acc:p10242]	Divided	5417.95	5924.41	1.09348	
1038	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]	Subtracted	5910.54	6440.58	530.04	
1039	myb-related protein b (b-myb). [source:swissprot;acc:p10244]	Divided	5418.92	5923.09	1.09304	
1039	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [source:swissprot;acc:q15814]	Subtracted	5719.01	6248.6	529.59	
1040	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [source:swissprot;acc:q9y305]	Subtracted	5719.01	6248.6	529.59	
1040	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	Divided	5421.93	5926.08	1.09298	
1041	dead-box protein. [source:refseq;acc:nm_018665]	Subtracted	5719.01	6248.6	529.59	
1041	myb-related protein a (a-myb). [source:swissprot;acc:p10243]	Divided	5419.18	5922.84	1.09294	
1042	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	Subtracted	3946.32	4475.47	529.15	
1042	similar to lim domain only 7 (fragment). [source:sptrembl;acc:q8n6m2]	Divided	5887.52	6434.32	1.09287	
1043	15 kda selenoprotein precursor. [source:swissprot;acc:o60613]	Divided	6344.41	6933.36	1.09283	
1043	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	Subtracted	3946.32	4475.47	529.15	
1044	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Subtracted	3946.32	4475.47	529.15	
1044	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [source:refseq;acc:nm_015517]	Divided	4757.46	5198.91	1.09279	
1045	histone h2b. [source:refseq;acc:nm_175055]	Subtracted	3946.32	4475.47	529.15	
1045	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [source:swissprot;acc:q14197]	Divided	5364.32	5862.09	1.09279	
1046	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	Subtracted	3946.32	4475.47	529.15	
1046	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [source:swissprot;acc:q9nzq9]	Divided	4757.46	5198.91	1.09279	
1047	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	Subtracted	3946.32	4475.47	529.15	
1047	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [source:swissprot;acc:q9nyl9]	Divided	4757.46	5198.91	1.09279	
1048	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	Subtracted	3946.32	4475.47	529.15	
1048	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [source:swissprot;acc:p28289]	Divided	4757.46	5198.91	1.09279	
1049	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [source:swissprot;acc:q9y5x1]	Divided	4757.46	5198.91	1.09279	
1049	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	Subtracted	3946.32	4475.47	529.15	
1050	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	Subtracted	3946.32	4475.47	529.15	
1050	neuronal tropomodulin (n-tmod) (tropomodulin 2). [source:swissprot;acc:q9nzr1]	Divided	4757.46	5198.91	1.09279	
1051	homeobox protein dlx-2. [source:swissprot;acc:q07687]	Divided	4757.46	5198.91	1.09279	
1051	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	Subtracted	5208.27	5737.17	528.9	
1052	homeobox protein dlx-5. [source:swissprot;acc:p56178]	Divided	4757.46	5198.91	1.09279	
1052	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	Subtracted	6278.76	6807.51	528.75	
1053	fetal brain protein 239 (239fb). [source:swissprot;acc:q15777]	Divided	4757.46	5198.91	1.09279	
1053	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Subtracted	5166.04	5694.55	528.51	
1054	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	Subtracted	5915.42	6443.77	528.35	
1054	homeobox protein dlx-3. [source:swissprot;acc:o60479]	Divided	4757.46	5198.91	1.09279	
1055	activated p21cdc42hs kinase. [source:refseq;acc:nm_005781]	Divided	4757.46	5198.91	1.09279	
1055	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	Subtracted	5167.15	5695.44	528.29	
1056	mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [source:refseq;acc:nm_015093]	Divided	4757.46	5198.91	1.09279	

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/