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 1713 to 1762 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1713	camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [source:swissprot;acc:p22694]	5917.23	6322.73	1.06853	
1714	camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [source:swissprot;acc:p17612]	5917.23	6322.73	1.06853	
1715	camp-dependent protein kinase type ii-beta regulatory chain. [source:swissprot;acc:p31323]	5918.48	6323.83	1.06849	
1716	inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [source:swissprot;acc:o14732]	6070.41	6485.85	1.06844	
1717	inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [source:swissprot;acc:p29218]	6069.65	6484.94	1.06842	
1718	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	9720.64	9099.1	1.06831	
1719	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [source:swissprot;acc:p34949]	5458.12	5830.76	1.06827	
1720	putative ankyrin-repeat containing protein. [source:refseq;acc:nm_025185]	5458.12	5830.76	1.06827	
1721	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	5458.12	5830.76	1.06827	
1722	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [source:swissprot;acc:q9nyq8]	5458.12	5830.76	1.06827	
1723	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [source:swissprot;acc:q14517]	5458.12	5830.76	1.06827	
1724	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [source:swissprot;acc:o95772]	5458.12	5830.76	1.06827	
1725	glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [source:swissprot;acc:p06744]	6051.06	6463.65	1.06818	
1726	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]	7048.79	7527.42	1.0679	
1727	phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [source:swissprot;acc:q9nry7]	6260.43	6685.05	1.06783	
1728	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6]	5475.44	5127.66	1.06782	
1729	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [source:swissprot;acc:q9nry6]	6259.8	6684.31	1.06782	
1730	phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [source:swissprot;acc:q9nrq2]	6259.8	6684.3	1.06781	
1731	lamin b2. [source:swissprot;acc:q03252]	5840.77	6236.53	1.06776	
1732	proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [source:swissprot;acc:q99436]	5781.8	6173.1	1.06768	
1733	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [source:swissprot;acc:p04720]	5874.83	6272.26	1.06765	
1734	zinc-finger protein zpr1 (zinc finger protein 259). [source:swissprot;acc:o75312]	5874.83	6272.26	1.06765	
1735	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [source:swissprot;acc:q05639]	5874.83	6272.26	1.06765	
1736	twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [source:refseq;acc:nm_021830]	5925.65	6326.43	1.06763	
1737	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [source:refseq;acc:nm_004703]	5925.65	6326.43	1.06763	
1738	ischemia/reperfusion inducible protein. [source:refseq;acc:nm_024640]	5885.08	6282.97	1.06761	
1739	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [source:swissprot;acc:p00966]	5695.57	6079.61	1.06743	
1740	serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [source:swissprot;acc:p53350]	5878.2	6274.27	1.06738	
1741	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [source:swissprot;acc:o15075]	6297.05	6721.08	1.06734	
1742	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	6298.76	6722.61	1.06729	
1743	histidine-rich membrane protein ke4. [source:swissprot;acc:q92504]	6298.81	6722.65	1.06729	
1744	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [source:swissprot;acc:q15691]	6298.81	6722.65	1.06729	
1745	microtubule-associated protein rp/eb family member 3 (protein eb3). [source:swissprot;acc:q9upy8]	6298.77	6722.62	1.06729	
1746	regucalcin gene promotor region related protein; rgpr-p117. [source:refseq;acc:nm_033127]	5683.17	6065.55	1.06728	
1747	cerebral cell adhesion molecule. [source:refseq;acc:nm_016174]	9596.59	10241.9	1.06724	
1748	doublecortin (lissencephalin-x) (lis-x) (doublin). [source:swissprot;acc:o43602]	6301.03	6724.63	1.06723	
1749	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [source:swissprot;acc:p13804]	7919.76	8452.01	1.06721	
1750	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [source:swissprot;acc:o15144]	5384.89	5746.51	1.06715	
1751	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [source:swissprot;acc:q92993]	6011.57	6414.98	1.06711	
1752	copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [source:swissprot;acc:q04656]	5941.29	6339.93	1.0671	
1753	eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [source:swissprot;acc:p20042]	5423.67	5787.46	1.06707	
1754	copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [source:swissprot;acc:p35670]	5941.83	6340.32	1.06707	
1755	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	7101.7	7577.75	1.06703	
1756	40s ribosomal protein s29. [source:swissprot;acc:p30054]	3582.57	3357.6	1.067	
1757	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	7101.15	7576.84	1.06699	
1758	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [source:refseq;acc:nm_004824]	7101.15	7576.84	1.06699	
1759	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	7101.16	7576.87	1.06699	
1760	thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [source:refseq;acc:nm_006472]	5693.88	6075.25	1.06698	
1761	electron transfer flavoprotein beta-subunit (beta-etf). [source:swissprot;acc:p38117]	7794.41	8316.04	1.06692	
1762	tumor susceptibility gene 101 protein. [source:swissprot;acc:q99816]	6122.76	6531.3	1.06672	

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/