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 3030 to 3079 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
1515	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868]	Divided	213.267	209.511	1.01793
1516	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]
	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282]	Subtracted	246.38	242.596	3.784
1517	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884]	Divided	213.267	209.511	1.01793
	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118]	Subtracted	213.274	209.5	3.774
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]	Divided	213.259	209.524	1.01783
	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119]	Subtracted	213.274	209.5	3.774
1519	cone-rod homeobox protein. [swissprot;acc:o43186]	Divided	244.331	240.061	1.01779
	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318]	Subtracted	217.785	214.021	3.764
1520	c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0]		212.103	208.339
	homeobox protein otx1. [swissprot;acc:p32242]	Divided	244.367	240.098	1.01778
1521	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1]	Subtracted	213.268	209.509	3.759
	homeobox protein otx2. [swissprot;acc:p32243]	Divided	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
	surfeit locus protein 1. [swissprot;acc:q15526]	Subtracted	213.268	209.509	3.759
1523	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]
	putative ankyrin-repeat containing protein. [refseq;acc:nm_025185]	Divided	219.306	223.179	1.01766
1524	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]
	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]	Subtracted	213.268	209.509	3.759
1525	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868]		213.267	209.511	3.756
	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8]	Divided	219.306	223.179	1.01766
1526	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Subtracted	213.267	209.511	3.756
1527	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]	Divided	219.306	223.179	1.01766
	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884]	Subtracted	213.267	209.511	3.756
1528	af-6 protein. [swissprot;acc:p55196]		218.733	214.98	3.753
	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318]	Divided	217.785	214.021	1.01759
1529	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]		216.762	213.031	1.01751
	myb proto-oncogene protein (c-myb). [swissprot;acc:p10242]	Subtracted	222.672	218.92	3.752
1530	af-6 protein. [swissprot;acc:p55196]	Divided	218.733	214.98	1.01746
	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	Subtracted	260.269	256.531	3.738
1531	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441]	Divided	217.025	213.304	1.01744
	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	Subtracted	225.159	221.424	3.735
1532	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]
	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]	Divided	228.419	232.376	1.01732
1533	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235]	Subtracted	225.159	221.424	3.735
	cytochrome c. [swissprot;acc:p00001]	Divided	228.419	232.376	1.01732
1534	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]
	[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]	Subtracted	213.259	209.524	3.735
1535	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141]		225.159	221.424
	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807]	Divided	228.419	232.376	1.01732
1536	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	Subtracted	216.762	213.031	3.731
	fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306]	Divided	228.419	232.376	1.01732
1537	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441]	Subtracted	217.025	213.304	3.721
	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312]	Divided	228.419	232.376	1.01732
1538	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
	myb-related protein b (b-myb). [swissprot;acc:p10244]	Subtracted	222.541	218.823	3.718
1539	myb-related protein a (a-myb). [swissprot;acc:p10243]		222.512	218.802	3.71
	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]	Divided	228.419	232.376	1.01732
1540	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966]	Subtracted	217.769	221.474	3.705

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.