MK5 Microarray Data

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

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Showing element 1518 to 1567 of 3228 in total

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

Rank	description	red	green	network_comparison
1518	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874]	213.259	209.524	1.01783
1519	cone-rod homeobox protein. [swissprot;acc:o43186]	244.331	240.061	1.01779
1520	homeobox protein otx1. [swissprot;acc:p32242]	244.367	240.098	1.01778
1521	homeobox protein otx2. [swissprot;acc:p32243]	244.478	240.212	1.01776
1522	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949]	219.306	223.179	1.01766
1523	putative ankyrin-repeat containing protein. [refseq;acc:nm_025185]
1524	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]
1525	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8]
1526	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]
1527	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]
1528	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318]	217.785	214.021	1.01759
1529	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	216.762	213.031	1.01751
1530	af-6 protein. [swissprot;acc:p55196]	218.733	214.98	1.01746
1531	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441]	217.025	213.304	1.01744
1532	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]	228.419	232.376	1.01732
1533	cytochrome c. [swissprot;acc:p00001]
1534	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]
1535	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807]
1536	fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306]
1537	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312]
1538	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
1539	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]
1540	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	240.077	236.015	1.01721
1541	myb proto-oncogene protein (c-myb). [swissprot;acc:p10242]	222.672	218.92	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). [swissprot;acc:q9nvh6]	213.546	209.965	1.01706
1543	gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
1544	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	219.762	216.081	1.01704
1545	orphan nuclear receptor tr2. [swissprot;acc:p13056]	219.76	216.083	1.01702
1546	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966]	217.769	221.474	1.01701
1547	myb-related protein b (b-myb). [swissprot;acc:p10244]	222.541	218.823	1.01699
1548	myb-related protein a (a-myb). [swissprot;acc:p10243]	222.512	218.802	1.01696
1549	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	225.159	221.424	1.01687
1550	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]
1551	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235]
1552	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141]
1553	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526]	215.389	211.833	1.01679
1554	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	196.215	193.018	1.01656
1555	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148]	196.192	192.996
1556	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]
1557	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]
1558	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	196.171	192.977	1.01655
1559	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	196.191	192.996
1560	p66 alpha. [refseq;acc:nm_017660]	167.687	170.455	1.01651
1561	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]
1562	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]
1563	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	218.277	214.739	1.01648
1564	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]
1565	eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5]	221.128	224.767	1.01646
1566	erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584]
1567	bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.