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 1463 to 1512 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1463	collagen alpha 3(iv) chain precursor (goodpasture antigen). [source:swissprot;acc:q01955]	5672.2	6103.92	1.07611	
1464	zasp protein (fragment). [source:sptrembl;acc:q9y4z3]	5671.93	6103.49	1.07609	
1465	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [source:swissprot;acc:p21695]	5686.74	6119.36	1.07608	
1466	proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [source:swissprot;acc:p28074]	6523.17	7019.44	1.07608	
1467	p47 protein isoform a. [source:refseq;acc:nm_016143]	6444.4	6932.39	1.07572	
1468	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [source:refseq;acc:nm_003901]	5473.09	5887.45	1.07571	
1469	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	5473.09	5887.45	1.07571	
1470	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [source:swissprot;acc:p04181]	5473.09	5887.45	1.07571	
1471	40s ribosomal protein s8. [source:swissprot;acc:p09058]	5659.45	6087.55	1.07564	
1472	26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [source:swissprot;acc:q15008]	5984.47	6435.42	1.07535	
1473	calmegin precursor. [source:swissprot;acc:o14967]	5910.06	6355.08	1.0753	
1474	calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [source:swissprot;acc:p27824]	5910.06	6355.08	1.0753	
1475	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	5910.06	6355.08	1.0753	
1476	rna (guanine-7-) methyltransferase. [source:refseq;acc:nm_003799]	5910.06	6355.08	1.0753	
1477	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	3687.37	3429.37	1.07523	
1478	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544]	5659.22	6084.68	1.07518	
1479	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [source:swissprot;acc:p55317]	5787.03	6221.72	1.07511	
1480	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [source:swissprot;acc:p15336]	5660.17	6085.22	1.07509	
1481	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	3688.8	3431.33	1.07504	
1482	leng5 protein. [source:refseq;acc:nm_024075]	5372.25	5775.21	1.07501	
1483	tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [source:swissprot;acc:p23381]	5372.25	5775.21	1.07501	
1484	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [source:refseq;acc:nm_006916]	5372.25	5775.21	1.07501	
1485	tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [source:swissprot;acc:q9ugm6]	5372.25	5775.21	1.07501	
1486	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [source:refseq;acc:nm_022445]	5372.25	5775.21	1.07501	
1487	nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [source:refseq;acc:nm_178177]	5573.64	5991.58	1.07499	
1488	delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [source:swissprot;acc:p54886]	5573.64	5991.58	1.07499	
1489	vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [source:swissprot;acc:p46459]	6192.38	6656.34	1.07492	
1490	f-actin capping protein alpha-1 subunit (capz alpha-1). [source:swissprot;acc:p52907]	6340.5	6815.41	1.0749	
1491	fidgetin-like 1. [source:refseq;acc:nm_022116]	6057.46	6510.9	1.07486	
1492	dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [source:swissprot;acc:p25205]	4619.81	4965.45	1.07482	
1493	deoxyhypusine synthase (ec 2.5.1.46) (dhs). [source:swissprot;acc:p49366]	6146.36	6606.21	1.07482	
1494	kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [source:swissprot;acc:q14145]	4619.81	4965.45	1.07482	
1495	nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [source:swissprot;acc:o96000]	6362.92	6838.6	1.07476	
1496	apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [source:refseq;acc:nm_032797]	5945.56	6389.63	1.07469	
1497	f-actin capping protein alpha-2 subunit (capz alpha-2). [source:swissprot;acc:p47755]	6339.08	6812.45	1.07467	
1498	40s ribosomal protein s13. [source:swissprot;acc:q02546]	5414.98	5818.7	1.07456	
1499	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [source:swissprot;acc:q9y261]	5798.31	6230.55	1.07455	
1500	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	10075.5	9377.75	1.0744	
1501	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	10075.5	9377.75	1.0744	
1502	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	10075.5	9377.75	1.0744	
1503	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	10075.5	9377.75	1.0744	
1504	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	10075.5	9377.75	1.0744	
1505	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	10075.5	9377.75	1.0744	
1506	hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [source:swissprot;acc:q9nzj6]	6152.78	6610.46	1.07439	
1507	atp synthase coupling factor b, mitochondrial precursor. [source:swissprot;acc:q99766]	6152.78	6610.46	1.07439	
1508	guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [source:swissprot;acc:q9y2t3]	6152.78	6610.46	1.07439	
1509	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:o00763]	7237.39	7775.21	1.07431	
1510	60s ribosomal protein l21. [source:swissprot;acc:p46778]	5546.11	5957.99	1.07426	
1511	serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [source:swissprot;acc:o00743]	7234.61	7771.58	1.07422	
1512	sporulation-induced transcript 4-associated protein. [source:refseq;acc:nm_018312]	7234.61	7771.58	1.07422	

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/