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

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Showing element 2713 to 2762 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1357	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	Divided	5657.71	6103.54	1.0788	
1357	flotillin-1. [source:swissprot;acc:o75955]	Subtracted	5655.85	6120.64	464.79	
1358	sestrin 1 (p53-regulated protein pa26). [source:swissprot;acc:q9y6p5]	Subtracted	5655.85	6120.62	464.77	
1358	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [source:swissprot;acc:q8n9l1]	Divided	5657.71	6103.54	1.0788	
1359	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	Divided	5657.71	6103.54	1.0788	
1359	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	Subtracted	5779.83	6244.56	464.73	
1360	calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [source:swissprot;acc:q14206]	Divided	5657.72	6103.52	1.07879	
1360	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]	Subtracted	6192.38	6656.34	463.96	
1361	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [source:swissprot;acc:q9uka8]	Divided	5657.72	6103.52	1.07879	
1361	u2 small nuclear ribonucleoprotein b". [source:swissprot;acc:p08579]	Subtracted	5675.96	6136.47	460.51	
1362	deoxyhypusine synthase (ec 2.5.1.46) (dhs). [source:swissprot;acc:p49366]	Subtracted	6146.36	6606.21	459.85	
1362	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [source:refseq;acc:nm_003900]	Divided	6322.75	6820.5	1.07872	
1363	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [source:swissprot;acc:p22307]	Divided	6322.75	6820.5	1.07872	
1363	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [source:swissprot;acc:p25787]	Subtracted	6343.76	6803.44	459.68	
1364	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [source:swissprot;acc:p54098]	Subtracted	5685.77	6145.43	459.66	
1364	protein c20orf4 (protein cgi-23) (pro0225). [source:swissprot;acc:q9y312]	Divided	5815.14	6272.66	1.07868	
1365	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070]	Subtracted	5589.33	6047.9	458.57	
1365	gamma adducin (adducin-like protein 70). [source:swissprot;acc:q9uey8]	Divided	5799.14	6255.04	1.07862	
1366	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	Subtracted	5589.33	6047.9	458.57	
1366	megf11 protein. [source:refseq;acc:nm_032445]	Divided	5793.55	6248.79	1.07858	
1367	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]	Subtracted	6152.78	6610.46	457.68	
1367	megf10 protein. [source:refseq;acc:nm_032446]	Divided	5793.47	6248.71	1.07858	
1368	atp synthase coupling factor b, mitochondrial precursor. [source:swissprot;acc:q99766]	Subtracted	6152.78	6610.46	457.68	
1368	beta adducin (erythrocyte adducin beta subunit). [source:swissprot;acc:p35612]	Divided	5793.29	6248.51	1.07858	
1369	alpha adducin (erythrocyte adducin alpha subunit). [source:swissprot;acc:p35611]	Divided	5786.71	6241.16	1.07853	
1369	guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [source:swissprot;acc:q9y2t3]	Subtracted	6152.78	6610.46	457.68	
1370	protein c20orf4 (protein cgi-23) (pro0225). [source:swissprot;acc:q9y312]	Subtracted	5815.14	6272.66	457.52	
1370	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	Divided	10231.8	9487.34	1.07847	
1371	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	Divided	10231.8	9487.34	1.07847	
1371	glycogenin-1 (ec 2.4.1.186). [source:swissprot;acc:p46976]	Subtracted	6376.12	6833.59	457.47	
1372	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [source:swissprot;acc:p55263]	Subtracted	6376.12	6833.59	457.47	
1372	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [source:refseq;acc:nm_004664]	Divided	5743.45	6193.45	1.07835	
1373	mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [source:swissprot;acc:p27361]	Divided	6079.85	6556.07	1.07833	
1373	protein x 0001. [source:refseq;acc:nm_016302]	Subtracted	6376.12	6833.59	457.47	
1374	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [source:swissprot;acc:o15488]	Subtracted	6376.12	6833.59	457.47	
1374	ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [source:swissprot;acc:p51812]	Divided	6079.45	6555.4	1.07829	
1375	calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [source:swissprot;acc:q13555]	Divided	6079.45	6555.4	1.07829	
1375	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [source:swissprot;acc:o60566]	Subtracted	5528.65	5985.58	456.93	
1376	calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [source:swissprot;acc:q13557]	Divided	6079.46	6555.41	1.07829	
1376	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Subtracted	5528.65	5985.58	456.93	
1377	mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [source:swissprot;acc:o95382]	Divided	6079.46	6555.4	1.07829	
1377	transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [source:swissprot;acc:p55072]	Subtracted	6449.02	6905.56	456.54	
1378	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [source:swissprot;acc:p00480]	Subtracted	5783.9	6240.19	456.29	
1378	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	Divided	6079.45	6555.4	1.07829	
1379	gamma adducin (adducin-like protein 70). [source:swissprot;acc:q9uey8]	Subtracted	5799.14	6255.04	455.9	
1379	ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [source:swissprot;acc:q15418]	Divided	6079.46	6555.41	1.07829	
1380	atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [source:swissprot;acc:p28288]	Divided	6079.46	6555.41	1.07829	
1380	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [source:refseq;acc:nm_014281]	Subtracted	6364.01	6819.38	455.37	
1381	glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [source:swissprot;acc:q92947]	Divided	6079.46	6555.41	1.07829	
1381	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [source:swissprot;acc:q13155]	Subtracted	6364.01	6819.38	455.37	

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/