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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1513 to 1562 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
1513	COX15	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [source:refseq;acc:nm_004376]	213.268	209.509	1.01794	
1514	COX10	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [source:swissprot;acc:q12887]	213.268	209.509	1.01794	
1515	DPP10	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	213.267	209.511	1.01793	
1516	DPP6	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	213.267	209.511	1.01793	
1517	FAP	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	213.267	209.511	1.01793	
1518	BCKDK	[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]	213.259	209.524	1.01783	
1519	CRX	cone-rod homeobox protein. [source:swissprot;acc:o43186]	244.331	240.061	1.01779	
1520	OTX1	homeobox protein otx1. [source:swissprot;acc:p32242]	244.367	240.098	1.01778	
1521	OTX2	homeobox protein otx2. [source:swissprot;acc:p32243]	244.478	240.212	1.01776	
1522	MPI	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [source:swissprot;acc:p34949]	219.306	223.179	1.01766	
1523		putative ankyrin-repeat containing protein. [source:refseq;acc:nm_025185]	219.306	223.179	1.01766	
1524	STARD3	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	219.306	223.179	1.01766	
1525	FAT2	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [source:swissprot;acc:q9nyq8]	219.306	223.179	1.01766	
1526	FAT	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [source:swissprot;acc:q14517]	219.306	223.179	1.01766	
1527	STARD3NL	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [source:swissprot;acc:o95772]	219.306	223.179	1.01766	
1528	FOXA3	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [source:swissprot;acc:p55318]	217.785	214.021	1.01759	
1529	ACTG1	actin, cytoplasmic 2 (gamma-actin). [source:swissprot;acc:p02571]	216.762	213.031	1.01751	
1530	MLLT4	af-6 protein. [source:swissprot;acc:p55196]	218.733	214.98	1.01746	
1531	CRIM1	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	217.025	213.304	1.01744	
1532	RBM10	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [source:swissprot;acc:p98175]	228.419	232.376	1.01732	
1533	CYCS	cytochrome c. [source:swissprot;acc:p00001]	228.419	232.376	1.01732	
1534	HS6ST2	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	228.419	232.376	1.01732	
1535	HS6ST1	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [source:refseq;acc:nm_004807]	228.419	232.376	1.01732	
1536	FA2H	fatty acid hydroxylase domain containing 1. [source:refseq;acc:nm_024306]	228.419	232.376	1.01732	
1537	WBP11	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [source:refseq;acc:nm_016312]	228.419	232.376	1.01732	
1538	ELAC2	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [source:refseq;acc:nm_018127]	228.419	232.376	1.01732	
1539	RBM5	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [source:swissprot;acc:p52756]	228.419	232.376	1.01732	
1540	ATG5	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	240.077	236.015	1.01721	
1541	MYB	myb proto-oncogene protein (c-myb). [source:swissprot;acc:p10242]	222.672	218.92	1.01714	
1542	TMLHE	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]	213.546	209.965	1.01706	
1543	ERAL1	gtp-binding protein era homolog (hera) (fragment). [source:swissprot;acc:o75616]	213.546	209.965	1.01706	
1544	NR2E1	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	219.762	216.081	1.01704	
1545	NR2C1	orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	219.76	216.083	1.01702	
1546	ASS1	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [source:swissprot;acc:p00966]	217.769	221.474	1.01701	
1547	MYBL2	myb-related protein b (b-myb). [source:swissprot;acc:p10244]	222.541	218.823	1.01699	
1548	MYBL1	myb-related protein a (a-myb). [source:swissprot;acc:p10243]	222.512	218.802	1.01696	
1549	DCTN2	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [source:swissprot;acc:q13561]	225.159	221.424	1.01687	
1550	SLC25A6	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	225.159	221.424	1.01687	
1551	SLC25A4	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [source:swissprot;acc:p12235]	225.159	221.424	1.01687	
1552	SLC25A5	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [source:swissprot;acc:p05141]	225.159	221.424	1.01687	
1553	AHCY	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	215.389	211.833	1.01679	
1554	CTBP1	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	196.215	193.018	1.01656	
1555	PASK	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [source:refseq;acc:nm_015148]	196.192	192.996	1.01656	
1556	BCL6	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	196.192	192.996	1.01656	
1557	SNAI2	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	196.192	192.996	1.01656	
1558	CTBP2	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	196.171	192.977	1.01655	
1559	BCL6B	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	196.191	192.996	1.01655	
1560	GATAD2A	p66 alpha. [source:refseq;acc:nm_017660]	167.687	170.455	1.01651	
1561	GATAD2B	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	167.687	170.455	1.01651	
1562		tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	167.687	170.455	1.01651	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/