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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 925 to 974 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
925	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [source:swissprot;acc:q15118]	5637.43	6193.07	1.09856	
926	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [source:swissprot;acc:q15119]	5637.45	6193.08	1.09856	
927	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	5638.64	6194.22	1.09853	
928	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [source:swissprot;acc:q9y6n1]	5638.46	6194.04	1.09853	
929	surfeit locus protein 1. [source:swissprot;acc:q15526]	5638.46	6194.04	1.09853	
930	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	5638.65	6194.23	1.09853	
931	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	5638.59	6194.17	1.09853	
932	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [source:refseq;acc:nm_004376]	5638.46	6194.04	1.09853	
933	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [source:swissprot;acc:q12887]	5638.46	6194.04	1.09853	
934	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [source:swissprot;acc:o14874]	5640	6195.52	1.0985	
935	neurotrimin precursor (hnt). [source:swissprot;acc:q9p121]	5413.63	5946.46	1.09842	
936	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	5628.21	6180.37	1.09811	
937	nucleobindin 1 precursor (calnuc). [source:swissprot;acc:q02818]	5859.25	6432.03	1.09776	
938	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	5859.25	6432.03	1.09776	
939	nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	5859.25	6432.03	1.09776	
940	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	5568.96	6113.35	1.09775	
941	caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [source:swissprot;acc:o75844]	4970.21	5455.34	1.09761	
942	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [source:swissprot;acc:p07205]	6597.56	7240.64	1.09747	
943	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [source:swissprot;acc:p09104]	6597.98	7241	1.09746	
944	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [source:swissprot;acc:p13929]	6597.98	7241	1.09746	
945	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [source:swissprot;acc:p06733]	6597.98	7241	1.09746	
946	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [source:swissprot;acc:p00558]	6598.37	7241.32	1.09744	
947	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	11797.1	10750.2	1.09738	
948	caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [source:swissprot;acc:p55210]	4633.48	5084.24	1.09728	
949	apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [source:swissprot;acc:p42574]	4633.48	5084.24	1.09728	
950	bystin. [source:swissprot;acc:q13895]	4280.99	4697.02	1.09718	
951	dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [source:swissprot;acc:p49326]	5364.3	5885.48	1.09716	
952	putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [source:swissprot;acc:o60774]	5364.3	5885.48	1.09716	
953	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	4906.33	5382.5	1.09705	
954	casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [source:swissprot;acc:p48729]	4906.33	5382.5	1.09705	
955	uridine kinase-like 1. [source:swissprot;acc:q9nwz5]	5548.78	6086.89	1.09698	
956	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	5364.77	5884.89	1.09695	
957	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [source:swissprot;acc:q08945]	4483.26	4917.77	1.09692	
958	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	4483.26	4917.77	1.09692	
959	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	4379.28	4803.59	1.09689	
960	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [source:swissprot;acc:q02156]	11773	10733.2	1.09688	
961	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [source:swissprot;acc:p23284]	11773	10733.2	1.09688	
962	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	11773	10733.2	1.09688	
963	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	11773	10733.2	1.09688	
964	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	11773	10733.2	1.09688	
965	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	11773.7	10733.8	1.09688	
966	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	7817.9	8575.12	1.09686	
967	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	7813.35	8569.96	1.09684	
968	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	7813.48	8570.11	1.09684	
969	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	7813.34	8569.95	1.09684	
970	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [source:swissprot;acc:q9y2j2]	7813.45	8570.07	1.09684	
971	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	7813.36	8569.97	1.09684	
972	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	7813.48	8570.11	1.09684	
973	galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	7810.11	8566.29	1.09682	
974	dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [source:swissprot;acc:q99518]	5365.06	5884.52	1.09682	

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/