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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3058 to 3107 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1529	myb proto-oncogene protein (c-myb). [source:swissprot;acc:p10242]	Subtracted	222.672	218.92	3.752	
1530	af-6 protein. [source:swissprot;acc:p55196]	Divided	218.733	214.98	1.01746	
1530	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [source:swissprot;acc:p30305]	Subtracted	260.269	256.531	3.738	
1531	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	Divided	217.025	213.304	1.01744	
1531	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [source: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). [source:swissprot;acc:p12236]	Subtracted	225.159	221.424	3.735	
1532	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [source: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). [source:swissprot;acc:p12235]	Subtracted	225.159	221.424	3.735	
1533	cytochrome c. [source:swissprot;acc:p00001]	Divided	228.419	232.376	1.01732	
1534	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	Divided	228.419	232.376	1.01732	
1534	[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]	Subtracted	213.259	209.524	3.735	
1535	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [source:swissprot;acc:p05141]	Subtracted	225.159	221.424	3.735	
1535	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [source:refseq;acc:nm_004807]	Divided	228.419	232.376	1.01732	
1536	actin, cytoplasmic 2 (gamma-actin). [source:swissprot;acc:p02571]	Subtracted	216.762	213.031	3.731	
1536	fatty acid hydroxylase domain containing 1. [source:refseq;acc:nm_024306]	Divided	228.419	232.376	1.01732	
1537	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	Subtracted	217.025	213.304	3.721	
1537	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [source: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. [source:refseq;acc:nm_018127]	Divided	228.419	232.376	1.01732	
1538	myb-related protein b (b-myb). [source:swissprot;acc:p10244]	Subtracted	222.541	218.823	3.718	
1539	myb-related protein a (a-myb). [source:swissprot;acc:p10243]	Subtracted	222.512	218.802	3.71	
1539	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [source:swissprot;acc:p52756]	Divided	228.419	232.376	1.01732	
1540	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [source:swissprot;acc:p00966]	Subtracted	217.769	221.474	3.705	
1540	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	Divided	240.077	236.015	1.01721	
1541	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [source:swissprot;acc:p55060]	Subtracted	192.336	188.637	3.699	
1541	myb proto-oncogene protein (c-myb). [source:swissprot;acc:p10242]	Divided	222.672	218.92	1.01714	
1542	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	Subtracted	219.762	216.081	3.681	
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]	Divided	213.546	209.965	1.01706	
1543	gtp-binding protein era homolog (hera) (fragment). [source:swissprot;acc:o75616]	Divided	213.546	209.965	1.01706	
1543	orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	Subtracted	219.76	216.083	3.677	
1544	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	Divided	219.762	216.081	1.01704	
1544	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [source:swissprot;acc:p04818]	Subtracted	225.119	228.769	3.65	
1545	dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	Subtracted	225.119	228.769	3.65	
1545	orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	Divided	219.76	216.083	1.01702	
1546	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [source:swissprot;acc:p00966]	Divided	217.769	221.474	1.01701	
1546	stromal cell-derived factor 2 precursor (sdf-2). [source:swissprot;acc:q99470]	Subtracted	225.119	228.769	3.65	
1547	myb-related protein b (b-myb). [source:swissprot;acc:p10244]	Divided	222.541	218.823	1.01699	
1547	stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [source:swissprot;acc:q9hcn8]	Subtracted	225.119	228.769	3.65	
1548	eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [source:swissprot;acc:q9ubq5]	Subtracted	221.128	224.767	3.639	
1548	myb-related protein a (a-myb). [source:swissprot;acc:p10243]	Divided	222.512	218.802	1.01696	
1549	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [source:swissprot;acc:q13561]	Divided	225.159	221.424	1.01687	
1549	erythroid differentiation and denucleation factor 1. [source:swissprot;acc:o60584]	Subtracted	221.128	224.767	3.639	
1550	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	Divided	225.159	221.424	1.01687	
1550	bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [source:refseq;acc:nm_176824]	Subtracted	221.128	224.767	3.639	
1551	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [source:swissprot;acc:p12235]	Divided	225.159	221.424	1.01687	
1551	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Subtracted	221.128	224.767	3.639	
1552	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [source:swissprot;acc:p05141]	Divided	225.159	221.424	1.01687	
1552	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	Subtracted	221.128	224.767	3.639	
1553	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	Divided	215.389	211.833	1.01679	
1553	protein c20orf45 (cgi-107). [source:swissprot;acc:q9y3b1]	Subtracted	221.128	224.767	3.639	
1554	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	Divided	196.215	193.018	1.01656	

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/