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 green red network_comparison
Results: HTML CSV LaTeX Showing element 2013 to 2062 of 3730 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
1511	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [source:swissprot;acc:q9y6n1]	209.509	213.268	1.01794	
1512	surfeit locus protein 1. [source:swissprot;acc:q15526]	209.509	213.268	1.01794	
1513	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [source:refseq;acc:nm_004376]	209.509	213.268	1.01794	
1514	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [source:swissprot;acc:q12887]	209.509	213.268	1.01794	
1515	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	209.511	213.267	1.01793	
1516	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	209.511	213.267	1.01793	
1517	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	209.511	213.267	1.01793	
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]	209.524	213.259	1.01783	
1519	cone-rod homeobox protein. [source:swissprot;acc:o43186]	240.061	244.331	1.01779	
1520	homeobox protein otx1. [source:swissprot;acc:p32242]	240.098	244.367	1.01778	
1521	homeobox protein otx2. [source:swissprot;acc:p32243]	240.212	244.478	1.01776	
1522	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [source:swissprot;acc:p34949]	223.179	219.306	1.01766	
1523	putative ankyrin-repeat containing protein. [source:refseq;acc:nm_025185]	223.179	219.306	1.01766	
1524	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	223.179	219.306	1.01766	
1525	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [source:swissprot;acc:q9nyq8]	223.179	219.306	1.01766	
1526	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [source:swissprot;acc:q14517]	223.179	219.306	1.01766	
1527	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [source:swissprot;acc:o95772]	223.179	219.306	1.01766	
1528	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [source:swissprot;acc:p55318]	214.021	217.785	1.01759	
1529	actin, cytoplasmic 2 (gamma-actin). [source:swissprot;acc:p02571]	213.031	216.762	1.01751	
1530	af-6 protein. [source:swissprot;acc:p55196]	214.98	218.733	1.01746	
1531	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	213.304	217.025	1.01744	
1532	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [source:swissprot;acc:p98175]	232.376	228.419	1.01732	
1533	cytochrome c. [source:swissprot;acc:p00001]	232.376	228.419	1.01732	
1534	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	232.376	228.419	1.01732	
1535	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [source:refseq;acc:nm_004807]	232.376	228.419	1.01732	
1536	fatty acid hydroxylase domain containing 1. [source:refseq;acc:nm_024306]	232.376	228.419	1.01732	
1537	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [source:refseq;acc:nm_016312]	232.376	228.419	1.01732	
1538	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [source:refseq;acc:nm_018127]	232.376	228.419	1.01732	
1539	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [source:swissprot;acc:p52756]	232.376	228.419	1.01732	
1540	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	236.015	240.077	1.01721	
1541	myb proto-oncogene protein (c-myb). [source:swissprot;acc:p10242]	218.92	222.672	1.01714	
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]	209.965	213.546	1.01706	
1543	gtp-binding protein era homolog (hera) (fragment). [source:swissprot;acc:o75616]	209.965	213.546	1.01706	
1544	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	216.081	219.762	1.01704	
1545	orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	216.083	219.76	1.01702	
1546	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [source:swissprot;acc:p00966]	221.474	217.769	1.01701	
1547	myb-related protein b (b-myb). [source:swissprot;acc:p10244]	218.823	222.541	1.01699	
1548	myb-related protein a (a-myb). [source:swissprot;acc:p10243]	218.802	222.512	1.01696	
1549	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [source:swissprot;acc:q13561]	221.424	225.159	1.01687	
1550	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	221.424	225.159	1.01687	
1551	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [source:swissprot;acc:p12235]	221.424	225.159	1.01687	
1552	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [source:swissprot;acc:p05141]	221.424	225.159	1.01687	
1553	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	211.833	215.389	1.01679	
1554	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	193.018	196.215	1.01656	
1555	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [source:refseq;acc:nm_015148]	192.996	196.192	1.01656	
1556	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	192.996	196.192	1.01656	
1557	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	192.996	196.192	1.01656	
1558	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	192.977	196.171	1.01655	
1559	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	192.996	196.191	1.01655	
1560	p66 alpha. [source:refseq;acc:nm_017660]	170.455	167.687	1.01651	

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/