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 Network Comparison Type Value Type description Filtered Interaction Map network_comparison green red

Results: HTML CSV LaTeX

Showing element 1508 to 1557 of 3228 in total

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

Rank	description	network_comparison	green	red	
1508	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [source:swissprot;acc:q15119]	1.01801	209.5	213.274	
1509	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [source:swissprot;acc:p42024]	1.01795	221.177	225.148	
1510	beta-centractin (actin-related protein 1b) (arp1b). [source:swissprot;acc:p42025]	1.01795	221.177	225.148	
1511	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [source:swissprot;acc:q9y6n1]	1.01794	209.509	213.268	
1512	surfeit locus protein 1. [source:swissprot;acc:q15526]	1.01794	209.509	213.268	
1513	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [source:refseq;acc:nm_004376]	1.01794	209.509	213.268	
1514	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [source:swissprot;acc:q12887]	1.01794	209.509	213.268	
1515	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	1.01793	209.511	213.267	
1516	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	1.01793	209.511	213.267	
1517	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	1.01793	209.511	213.267	
1518	[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]	1.01783	209.524	213.259	
1519	cone-rod homeobox protein. [source:swissprot;acc:o43186]	1.01779	240.061	244.331	
1520	homeobox protein otx1. [source:swissprot;acc:p32242]	1.01778	240.098	244.367	
1521	homeobox protein otx2. [source:swissprot;acc:p32243]	1.01776	240.212	244.478	
1522	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [source:swissprot;acc:p34949]	1.01766	223.179	219.306	
1523	putative ankyrin-repeat containing protein. [source:refseq;acc:nm_025185]	1.01766	223.179	219.306	
1524	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	1.01766	223.179	219.306	
1525	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [source:swissprot;acc:q9nyq8]	1.01766	223.179	219.306	
1526	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [source:swissprot;acc:q14517]	1.01766	223.179	219.306	
1527	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [source:swissprot;acc:o95772]	1.01766	223.179	219.306	
1528	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [source:swissprot;acc:p55318]	1.01759	214.021	217.785	
1529	actin, cytoplasmic 2 (gamma-actin). [source:swissprot;acc:p02571]	1.01751	213.031	216.762	
1530	af-6 protein. [source:swissprot;acc:p55196]	1.01746	214.98	218.733	
1531	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	1.01744	213.304	217.025	
1532	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [source:swissprot;acc:p98175]	1.01732	232.376	228.419	
1533	cytochrome c. [source:swissprot;acc:p00001]	1.01732	232.376	228.419	
1534	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	1.01732	232.376	228.419	
1535	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [source:refseq;acc:nm_004807]	1.01732	232.376	228.419	
1536	fatty acid hydroxylase domain containing 1. [source:refseq;acc:nm_024306]	1.01732	232.376	228.419	
1537	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [source:refseq;acc:nm_016312]	1.01732	232.376	228.419	
1538	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [source:refseq;acc:nm_018127]	1.01732	232.376	228.419	
1539	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [source:swissprot;acc:p52756]	1.01732	232.376	228.419	
1540	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	1.01721	236.015	240.077	
1541	myb proto-oncogene protein (c-myb). [source:swissprot;acc:p10242]	1.01714	218.92	222.672	
1542	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]	1.01706	209.965	213.546	
1543	gtp-binding protein era homolog (hera) (fragment). [source:swissprot;acc:o75616]	1.01706	209.965	213.546	
1544	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	1.01704	216.081	219.762	
1545	orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	1.01702	216.083	219.76	
1546	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [source:swissprot;acc:p00966]	1.01701	221.474	217.769	
1547	myb-related protein b (b-myb). [source:swissprot;acc:p10244]	1.01699	218.823	222.541	
1548	myb-related protein a (a-myb). [source:swissprot;acc:p10243]	1.01696	218.802	222.512	
1549	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [source:swissprot;acc:q13561]	1.01687	221.424	225.159	
1550	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	1.01687	221.424	225.159	
1551	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [source:swissprot;acc:p12235]	1.01687	221.424	225.159	
1552	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [source:swissprot;acc:p05141]	1.01687	221.424	225.159	
1553	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	1.01679	211.833	215.389	
1554	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	1.01656	193.018	196.215	
1555	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [source:refseq;acc:nm_015148]	1.01656	192.996	196.192	
1556	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	1.01656	192.996	196.192	
1557	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	1.01656	192.996	196.192	

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/