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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
1276	CHRNA3	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [source:swissprot;acc:p32297]	Divided	171.231	167.177	1.02425	
1276	PPP3CB	serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [source:swissprot;acc:p16299]	Subtracted	218.44	213.44	5	
1277	POLE3	dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [source:swissprot;acc:q9nrf9]	Subtracted	250.854	255.842	4.988	
1277	SPHK2	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]	Divided	171.231	167.177	1.02425	
1278	NDST2	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [source:swissprot;acc:p52849]	Subtracted	228.409	223.475	4.934	
1278	SESN3	sestrin 3. [source:swissprot;acc:p58005]	Divided	218.368	213.219	1.02415	
1279	NDST3	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784]	Subtracted	228.409	223.475	4.934	
1279	SESN2	sestrin 2 (hi95). [source:swissprot;acc:p58004]	Divided	218.368	213.219	1.02415	
1280	CYP4A11	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [source:swissprot;acc:q02928]	Divided	218.368	213.22	1.02414	
1280	NDST4	n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569]	Subtracted	228.409	223.475	4.934	
1281	CYP4F3	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:q08477]	Divided	218.368	213.22	1.02414	
1281	NDST1	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [source:swissprot;acc:p52848]	Subtracted	228.409	223.475	4.934	
1282	CDC27	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	Subtracted	228.409	223.475	4.934	
1282	CYP4F8	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Divided	218.368	213.22	1.02414	
1283	CYP4X1	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	Divided	218.368	213.22	1.02414	
1283	DLAT	dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [source:swissprot;acc:p10515]	Subtracted	206.482	211.404	4.922	
1284	CYP4F12	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	Divided	218.368	213.22	1.02414	
1284	GSTT2B	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Subtracted	228.642	223.726	4.916	
1285	CYP4F2	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	Divided	218.368	213.22	1.02414	
1285	TGFBR1	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [source:swissprot;acc:p36897]	Subtracted	223.89	228.805	4.915	
1286	ACVR1B	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [source:swissprot;acc:p36896]	Subtracted	223.885	228.797	4.912	
1286	CYP4F11	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	Divided	218.368	213.22	1.02414	
1287	CYP4A22	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [source:sptrembl;acc:q9ntl5]	Divided	218.368	213.22	1.02414	
1287	FREQ	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [source:swissprot;acc:p36610]	Subtracted	223.887	228.799	4.912	
1288	ACVR1C	activin a receptor, type ic; activin receptor-like kinase 7. [source:refseq;acc:nm_145259]	Subtracted	223.884	228.795	4.911	
1288	CYP4B1	cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [source:swissprot;acc:p13584]	Divided	218.368	213.22	1.02414	
1289	FLOT1	flotillin-1. [source:swissprot;acc:o75955]	Divided	218.368	213.22	1.02414	
1289	PAOX	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	Subtracted	228.644	223.736	4.908	
1290	ATPIF1	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	Subtracted	228.644	223.736	4.908	
1290	SESN1	sestrin 1 (p53-regulated protein pa26). [source:swissprot;acc:q9y6p5]	Divided	218.368	213.22	1.02414	
1291	HAS2	hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [source:swissprot;acc:q92819]	Divided	221.093	226.399	1.024	
1291	SMOX	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [source:refseq;acc:nm_019025]	Subtracted	228.644	223.736	4.908	
1292	CASP7	caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [source:swissprot;acc:p55210]	Divided	233.942	228.46	1.024	
1292	HCCS	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701]	Subtracted	228.644	223.736	4.908	
1293	CASP3	apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [source:swissprot;acc:p42574]	Divided	233.942	228.46	1.024	
1293	TPD52L2	tumor protein d54 (hd54) (d52-like 2). [source:swissprot;acc:o43399]	Subtracted	206.852	211.757	4.905	
1294	GSTT1	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711]	Subtracted	228.646	223.744	4.902	
1294	HAS1	hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [source:swissprot;acc:q92839]	Divided	221.093	226.399	1.024	
1295	HAS3	hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [source:swissprot;acc:o00219]	Divided	221.093	226.399	1.024	
1295	OXA1L	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070]	Subtracted	220.681	215.78	4.901	
1296	MRPL34	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	Subtracted	220.681	215.78	4.901	
1296	SLC37A1	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057]	Divided	209.062	204.174	1.02394	
1297	PRODH	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272]	Divided	209.062	204.174	1.02394	
1297	SF3B4	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source:swissprot;acc:q15427]	Subtracted	232.752	237.65	4.898	
1298	DLAT	dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [source:swissprot;acc:p10515]	Divided	206.482	211.404	1.02384	
1298	SLC37A1	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057]	Subtracted	209.062	204.174	4.888	
1299	GSR	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [source:swissprot;acc:p00390]	Subtracted	207.387	212.275	4.888	
1299	PMPCB	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [source:swissprot;acc:o75439]	Divided	217.635	212.575	1.0238	
1300	PMPCA	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [source:swissprot;acc:q10713]	Divided	217.634	212.576	1.02379	
1300	PRODH	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272]	Subtracted	209.062	204.174	4.888	

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/