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	network_comparison	green

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Showing element 1525 to 1574 of 3228 in total

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

Rank	description	red	network_comparison	green
1525	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8]	219.306	1.01766	223.179
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	1.01759	214.021
1529	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	216.762	1.01751	213.031
1530	af-6 protein. [swissprot;acc:p55196]	218.733	1.01746	214.98
1531	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441]	217.025	1.01744	213.304
1532	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]	228.419	1.01732	232.376
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	1.01721	236.015
1541	myb proto-oncogene protein (c-myb). [swissprot;acc:p10242]	222.672	1.01714	218.92
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	1.01706	209.965
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	1.01704	216.081
1545	orphan nuclear receptor tr2. [swissprot;acc:p13056]	219.76	1.01702	216.083
1546	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966]	217.769	1.01701	221.474
1547	myb-related protein b (b-myb). [swissprot;acc:p10244]	222.541	1.01699	218.823
1548	myb-related protein a (a-myb). [swissprot;acc:p10243]	222.512	1.01696	218.802
1549	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	225.159	1.01687	221.424
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	1.01679	211.833
1554	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	196.215	1.01656	193.018
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	1.01655	192.977
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	1.01651	170.455
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	1.01648	214.739
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	1.01646	224.767
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]
1568	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]
1569	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
1570	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]
1571	eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]
1572	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]
1573	r3h domain protein 1. [swissprot;acc:q15032]	218.105		214.573
1574	tata element modulatory factor (tmf). [swissprot;acc:p82094]	222.585	1.01645	218.982

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.