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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Value Type Interaction Map description Network Comparison Type Rank Gene red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1975 to 2024 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	1006	5707.73	6249.1	1.09485	
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [source:swissprot;acc:q13162]	1302	6343.26	6862.94	1.08193	
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [source:swissprot;acc:p30044]	2544	6239.69	6378.35	1.02222	
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [source:swissprot;acc:o75521]	1726	7048.79	7527.42	1.0679	
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [source:refseq;acc:nm_152331]	1987	5829.74	6175.69	1.05934	
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [source:swissprot;acc:p49753]	1984	5830.03	6176.1	1.05936	
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	876	5644.68	6223.23	1.10249	
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	530	8600.02	9792.49	1.13866	
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [source:swissprot;acc:q9nr77]	1276	6437.99	6969.67	1.08258	
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [source:swissprot;acc:o75381]	1440	6522.96	7023.77	1.07678	
peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	641	4810.85	5414.21	1.12542	
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]	1016	5791.82	6340.86	1.0948	
peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [source:swissprot;acc:o00628]	2573	7056.58	7194.99	1.01961	
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	2231	3650.8	3484.94	1.04759	
pescadillo homolog 1. [source:swissprot;acc:o00541]	447	3751.14	4310.89	1.14922	
phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	1273	5885	6371.14	1.08261	
phd finger protein 9. [source:refseq;acc:nm_018062]	2171	5825.61	6126.74	1.05169	
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	1963	4374.32	4126.96	1.05994	
phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	725	5384.41	6012.82	1.11671	
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	724	5384.41	6012.82	1.11671	
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [source:swissprot;acc:q9nsd9]	1102	5462.88	5958.12	1.09066	
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [source:swissprot;acc:p11086]	1671	5791.14	6193.02	1.0694	
phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	2193	5285.38	5034.86	1.04976	
phosducin-like protein (phlp). [source:swissprot;acc:q13371]	2190	5285.38	5034.86	1.04976	
phosphate carrier protein, mitochondrial precursor (ptp). [source:swissprot;acc:q00325]	3176	0.00001	0.00001	1	
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	1075	6441.56	7034.86	1.09211	
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [source:swissprot;acc:o95674]	1084	6437.49	7029.22	1.09192	
phosphatidylethanolamine-binding protein (pebp) (prostatic binding protein) (hcnppp) (neuropolypeptide h3) (raf kinase inhibitor protein) (rkip) [contains: hippocampal cholinergic neurostimulating peptide (hcnp)]. [source:swissprot;acc:p30086]	3162	0.00001	0.00001	1	
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [source:swissprot;acc:p27986]	865	5595.65	6173.23	1.10322	
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [source:swissprot;acc:o00459]	870	5595.65	6173.23	1.10322	
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [source:swissprot;acc:q92569]	867	5595.65	6173.23	1.10322	
phosphatidylinositol glycan class t precursor. [source:refseq;acc:nm_015937]	3024	0.00001	0.00001	1	
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	1701	6326.24	6762.27	1.06892	
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [source:swissprot;acc:o75747]	1700	6326.24	6762.27	1.06892	
phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	2290	5783.75	6048.93	1.04585	
phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	586	6739.81	7644.62	1.13425	
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [source:swissprot;acc:o95394]	1603	5232.14	5605.8	1.07142	
phosphofurin acidic cluster sorting protein 1 isoform 1; cytosolic sorting protein pacs-1. [source:refseq;acc:nm_018026]	2805	0.00001	0.00001	1	
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [source:swissprot;acc:p00558]	946	6598.37	7241.32	1.09744	
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [source:swissprot;acc:p07205]	942	6597.56	7240.64	1.09747	
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	1113	5910.54	6440.58	1.08968	
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [source:swissprot;acc:p15259]	1114	5910.54	6440.58	1.08968	
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [source:refseq;acc:nm_002645]	1703	6326.24	6762.27	1.06892	
phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [source:refseq;acc:nm_002647]	3173	0.00001	0.00001	1	
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [source:swissprot;acc:q13393]	1622	6153.79	6589.52	1.07081	
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [source:swissprot;acc:o14939]	1626	6157.13	6591.53	1.07055	
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [source:swissprot;acc:q9nry7]	1727	6260.43	6685.05	1.06783	
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [source:swissprot;acc:q9nry6]	1729	6259.8	6684.31	1.06782	
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [source:swissprot;acc:q9nrq2]	1730	6259.8	6684.3	1.06781	
phospholipid transfer protein precursor (lipid transfer protein ii). [source:swissprot;acc:p55058]	2339	5123.89	5350.78	1.04428	

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/