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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1875 to 1924 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
938	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	Divided	5859.25	6432.03	1.09776	
938	tumor differentially expressed 1 protein like. [source:swissprot;acc:q9nrx5]	Subtracted	6133.83	6690.18	556.35	
939	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [source:swissprot;acc:o43175]	Subtracted	6133.83	6690.18	556.35	
939	nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	Divided	5859.25	6432.03	1.09776	
940	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	Divided	5568.96	6113.35	1.09775	
940	transducin-like enhancer protein 3 (esg3). [source:swissprot;acc:q04726]	Subtracted	6280.74	6837.01	556.27	
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]	Divided	4970.21	5455.34	1.09761	
941	paraspeckle protein 1. [source:refseq;acc:nm_018282]	Subtracted	10241.3	9685.21	556.09	
942	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [source:swissprot;acc:p07205]	Divided	6597.56	7240.64	1.09747	
942	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [source:swissprot;acc:q15118]	Subtracted	5637.43	6193.07	555.64	
943	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [source:swissprot;acc:p09104]	Divided	6597.98	7241	1.09746	
943	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [source:swissprot;acc:q15119]	Subtracted	5637.45	6193.08	555.63	
944	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [source:swissprot;acc:p13929]	Divided	6597.98	7241	1.09746	
944	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	Subtracted	5638.64	6194.22	555.58	
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]	Divided	6597.98	7241	1.09746	
945	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [source:swissprot;acc:q9y6n1]	Subtracted	5638.46	6194.04	555.58	
946	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [source:swissprot;acc:p00558]	Divided	6598.37	7241.32	1.09744	
946	surfeit locus protein 1. [source:swissprot;acc:q15526]	Subtracted	5638.46	6194.04	555.58	
947	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	Subtracted	5638.65	6194.23	555.58	
947	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	Divided	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]	Divided	4633.48	5084.24	1.09728	
948	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	Subtracted	5638.59	6194.17	555.58	
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]	Divided	4633.48	5084.24	1.09728	
949	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [source:refseq;acc:nm_004376]	Subtracted	5638.46	6194.04	555.58	
950	bystin. [source:swissprot;acc:q13895]	Divided	4280.99	4697.02	1.09718	
950	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [source:swissprot;acc:q12887]	Subtracted	5638.46	6194.04	555.58	
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]	Divided	5364.3	5885.48	1.09716	
951	[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]	Subtracted	5640	6195.52	555.52	
952	interleukin-4 induced protein 1 precursor (fig-1 protein). [source:swissprot;acc:q96rq9]	Subtracted	5800.95	6355.71	554.76	
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]	Divided	5364.3	5885.48	1.09716	
953	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	Divided	4906.33	5382.5	1.09705	
953	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [source:refseq;acc:nm_003400]	Subtracted	5195.58	5750.34	554.76	
954	casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [source:swissprot;acc:p48729]	Divided	4906.33	5382.5	1.09705	
954	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	Subtracted	3760.8	4315.06	554.26	
955	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	Subtracted	3760.8	4315.06	554.26	
955	uridine kinase-like 1. [source:swissprot;acc:q9nwz5]	Divided	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]	Divided	5364.77	5884.89	1.09695	
956	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Subtracted	3760.8	4315.06	554.26	
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]	Divided	4483.26	4917.77	1.09692	
957	transducin-like enhancer protein 4. [source:swissprot;acc:q04727]	Subtracted	6270.67	6823.73	553.06	
958	block of proliferation 1. [source:swissprot;acc:q14137]	Subtracted	3796.24	4348.59	552.35	
958	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	Divided	4483.26	4917.77	1.09692	
959	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Subtracted	5628.21	6180.37	552.16	
959	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	Divided	4379.28	4803.59	1.09689	
960	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [source:swissprot;acc:q02156]	Divided	11773	10733.2	1.09688	
960	trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [source:swissprot;acc:q9nvh6]	Subtracted	6410.73	6962.22	551.49	
961	gtp-binding protein era homolog (hera) (fragment). [source:swissprot;acc:o75616]	Subtracted	6410.73	6962.22	551.49	
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]	Divided	11773	10733.2	1.09688	
962	transcription factor smif; decapping enzyme hdcp1a. [source:refseq;acc:nm_018403]	Subtracted	5172.07	5723.22	551.15	
962	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	Divided	11773	10733.2	1.09688	

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/