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.


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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2425 to 2474 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
607	bet3 homolog. [source:swissprot;acc:o43617]	Rooted	116.061	125.434	1.08076	
607	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [source:swissprot;acc:q96kp4]	Squared	26583.8	31468.6	1.18375	
607	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Ranked	247.47	233.441	1.0601	
607	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	Measured	14976.4	13246.6	1.13058	
608	histone h2b. [source:refseq;acc:nm_175055]	Ranked	247.47	233.441	1.0601	
608	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [source:swissprot;acc:p22570]	Squared	24560.6	29071.1	1.18365	
608	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	Measured	4510.61	5098.74	1.13039	
608	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	Rooted	59.6517	64.4642	1.08068	
609	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Measured	3886.62	3438.82	1.13022	
609	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	Ranked	247.47	233.441	1.0601	
609	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	Rooted	62.9281	67.99	1.08044	
609	pyrroline 5-carboxylate reductase isoform. [source:refseq;acc:nm_013328]	Squared	12276.9	14526	1.1832	
610	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Rooted	136.706	126.565	1.08012	
610	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	Ranked	247.47	233.441	1.0601	
610	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	Measured	8430.03	9518.11	1.12907	
610	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	Squared	12347.6	14594.8	1.18199	
611	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	Squared	23487.1	27726.3	1.18049	
611	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	Measured	5148.71	5811.74	1.12878	
611	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	Ranked	247.47	233.441	1.0601	
611	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	Rooted	51.0091	55.0909	1.08002	
612	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	Measured	3975.77	4485.05	1.1281	
612	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	Rooted	57.1949	61.7633	1.07987	
612	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	Ranked	247.47	233.441	1.0601	
612	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Squared	18595.6	21936.3	1.17965	
613	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	Ranked	247.47	233.441	1.0601	
613	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	Rooted	57.1971	61.7626	1.07982	
613	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [source:swissprot;acc:p41227]	Squared	17550.2	20701.1	1.17954	
613	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Measured	3975.77	4485.05	1.1281	
614	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	Squared	51527.6	43689.1	1.17942	
614	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	Rooted	57.2007	61.7615	1.07973	
614	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	Ranked	214.257	202.125	1.06002	
614	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [source:refseq;acc:nm_018158]	Measured	11222.2	9948.93	1.12798	
615	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	Squared	51527.6	43689.1	1.17942	
615	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	Measured	11222.2	9948.93	1.12798	
615	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [source:swissprot;acc:q06545]	Rooted	57.2007	61.7615	1.07973	
615	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	Ranked	214.257	202.132	1.05999	
616	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	Measured	11222.2	9948.93	1.12798	
616	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	Squared	51527.6	43689.1	1.17942	
616	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	Ranked	214.257	202.132	1.05999	
616	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [source:swissprot;acc:o00217]	Rooted	57.2007	61.7615	1.07973	
617	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	Squared	51527.6	43689.1	1.17942	
617	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Measured	5162.52	5822.47	1.12783	
617	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	Rooted	57.2008	61.7614	1.07973	
617	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	Ranked	214.257	202.135	1.05997	
618	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	Ranked	214.256	202.139	1.05994	
618	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	Rooted	57.208	61.7592	1.07956	
618	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Measured	7878.27	8879.08	1.12703	
618	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	Squared	51527.6	43689.1	1.17942	
619	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	Squared	51527.6	43689.1	1.17942	
619	dendritic cell protein. [source:refseq;acc:nm_006360]	Rooted	63.847	68.8873	1.07894	

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/