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 1001 to 1050 of 3228 in total

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

Rank	description	red	green	network_comparison	
1001	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [source:swissprot;acc:p38571]	5680.76	6220.45	1.095	
1002	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [source:swissprot;acc:q9np81]	5680.76	6220.45	1.095	
1003	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [source:swissprot;acc:p49591]	5680.76	6220.45	1.095	
1004	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	5391.64	5903.72	1.09498	
1005	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	5780.34	6329.3	1.09497	
1006	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	5707.73	6249.1	1.09485	
1007	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	5707.73	6249.1	1.09485	
1008	single-minded homolog 1. [source:swissprot;acc:p81133]	5707.73	6249.1	1.09485	
1009	synapsin iii. [source:swissprot;acc:o14994]	5791.82	6340.86	1.0948	
1010	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	5791.82	6340.86	1.0948	
1011	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [source:swissprot;acc:q9y5j3]	5791.82	6340.86	1.0948	
1012	actin binding lim protein 2. [source:refseq;acc:nm_032432]	5791.82	6340.86	1.0948	
1013	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	5791.82	6340.86	1.0948	
1014	synapsin ii. [source:swissprot;acc:q92777]	5791.82	6340.86	1.0948	
1015	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	5791.82	6340.86	1.0948	
1016	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]	5791.82	6340.86	1.0948	
1017	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	5791.82	6340.86	1.0948	
1018	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	5791.82	6340.86	1.0948	
1019	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	5791.82	6340.86	1.0948	
1020	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	5791.82	6340.86	1.0948	
1021	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	5791.82	6340.86	1.0948	
1022	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [source:swissprot;acc:p49760]	6435.94	7045.75	1.09475	
1023	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [source:swissprot;acc:p49761]	6435.02	7044.65	1.09474	
1024	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [source:swissprot;acc:p50238]	5706.5	6245.55	1.09446	
1025	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [source:swissprot;acc:o15305]	5511.96	6031.95	1.09434	
1026	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [source:swissprot;acc:q92871]	5509.89	6029.29	1.09427	
1027	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [source:swissprot;acc:p31153]	6123.15	6700.05	1.09422	
1028	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [source:swissprot;acc:q15274]	5704	6241.36	1.09421	
1029	beta-catenin (pro2286). [source:swissprot;acc:p35222]	5635.26	6166.09	1.0942	
1030	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [source:swissprot;acc:p49674]	5048.33	5523.85	1.09419	
1031	membrane protein expressed in epithelial-like lung adenocarcinoma. [source:refseq;acc:nm_024792]	6136.99	6714.98	1.09418	
1032	ran binding protein 11. [source:refseq;acc:nm_016338]	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]	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	

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/