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 1630 to 1679 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
815	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	Subtracted	5786.67	6395.78	609.11	
816	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Subtracted	5786.67	6395.78	609.11	
816	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [source:refseq;acc:nm_144678]	Divided	5641.53	6256.17	1.10895	
817	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p36542]	Subtracted	5657.53	6263.02	605.49	
817	ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	Divided	6811.2	7547.35	1.10808	
818	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [source:refseq;acc:nm_005763]	Divided	6807.78	7543.28	1.10804	
818	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [source:swissprot;acc:p48047]	Subtracted	5657.53	6263.02	605.49	
819	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [source:swissprot;acc:p56559]	Subtracted	5912.84	6517.69	604.85	
819	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	Divided	6805.45	7540.5	1.10801	
820	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	Divided	6805.86	7540.99	1.10801	
820	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [source:swissprot;acc:p12953]	Subtracted	5912.84	6517.69	604.85	
821	adp-ribosylation factor-like protein 4. [source:swissprot;acc:p40617]	Subtracted	5912.84	6517.69	604.85	
821	trna isopentenylpyrophosphate transferase. [source:refseq;acc:nm_017646]	Divided	6257.99	6932.95	1.10786	
822	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Subtracted	4811.02	5414.64	603.62	
822	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Divided	6311.6	6989.33	1.10738	
823	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	Subtracted	4810.85	5414.23	603.38	
823	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	Divided	6311.83	6989.6	1.10738	
824	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p36542]	Divided	5657.53	6263.02	1.10702	
824	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	4810.85	5414.23	603.38	
825	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [source:swissprot;acc:p48047]	Divided	5657.53	6263.02	1.10702	
825	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701]	Subtracted	4810.85	5414.22	603.37	
826	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [source:refseq;acc:nm_003400]	Divided	5195.58	5750.34	1.10678	
826	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	Subtracted	4810.85	5414.21	603.36	
827	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711]	Subtracted	4810.71	5413.89	603.18	
827	transcription factor smif; decapping enzyme hdcp1a. [source:refseq;acc:nm_018403]	Divided	5172.07	5723.22	1.10656	
828	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [source:swissprot;acc:p55786]	Divided	5745.61	6354.75	1.10602	
828	upstream binding protein 1 (lbp-1a). [source:refseq;acc:nm_014517]	Subtracted	5903.18	6506.32	603.14	
829	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [source:swissprot;acc:p09960]	Divided	5745.61	6354.75	1.10602	
829	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Subtracted	5903.18	6506.32	603.14	
830	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [source:swissprot;acc:q02127]	Divided	5745.61	6354.75	1.10602	
830	lbp-9. [source:refseq;acc:nm_014553]	Subtracted	5903.18	6506.32	603.14	
831	splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [source:swissprot;acc:p23152]	Subtracted	5903.18	6506.32	603.14	
831	t-cell activation wd repeat protein. [source:refseq;acc:nm_139281]	Divided	4062.03	4492.48	1.10597	
832	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	Divided	4489.72	4965.35	1.10594	
832	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	Subtracted	5929.48	6531.48	602	
833	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [source:refseq;acc:nm_139279]	Subtracted	5929.55	6531.52	601.97	
833	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	Divided	4489.72	4965.35	1.10594	
834	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p25705]	Divided	5623.18	6218.77	1.10592	
834	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [source:sptrembl;acc:q9ujn8]	Subtracted	5929.55	6531.52	601.97	
835	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [source:swissprot;acc:q9nvs2]	Divided	5623.18	6218.77	1.10592	
835	histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	Subtracted	5929.61	6531.55	601.94	
836	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	Divided	4049	4477.43	1.10581	
836	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [source:swissprot;acc:q16781]	Subtracted	6229.69	6829.58	599.89	
837	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	Divided	4063.64	4492.98	1.10565	
837	kinesin family member c3. [source:refseq;acc:nm_005550]	Subtracted	5995.49	6595.35	599.86	
838	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057]	Subtracted	6520.28	7119.28	599	
838	pbk1 protein. [source:sptrembl;acc:o76021]	Divided	4064.23	4493.36	1.10559	
839	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	Divided	7093.86	7842.67	1.10556	
839	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272]	Subtracted	6520.28	7119.28	599	
840	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	Subtracted	10300	9701.33	598.67	

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/