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 1677 to 1726 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1677	ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [source:swissprot;acc:o75792]	6075.19	6496.61	1.06937	
1678	cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [source:refseq;acc:nm_007006]	5763.25	6162.98	1.06936	
1679	proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [source:swissprot;acc:p49720]	6180.24	6608.11	1.06923	
1680	methylenetetrahydrofolate reductase (ec 1.5.1.20). [source:swissprot;acc:p42898]	6436.73	6882.16	1.0692	
1681	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [source:swissprot;acc:q96kx2]	6304.74	6740.66	1.06914	
1682	f-actin capping protein beta subunit (capz beta). [source:swissprot;acc:p47756]	6304.74	6740.66	1.06914	
1683	ring finger protein 20. [source:refseq;acc:nm_019592]	5419.54	5793.94	1.06908	
1684	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [source:refseq;acc:nm_014771]	5419.54	5793.94	1.06908	
1685	gc-rich sequence dna-binding factor homolog. [source:swissprot;acc:q9y5b6]	6088.07	6508.45	1.06905	
1686	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [source:swissprot;acc:o60603]	6088.07	6508.45	1.06905	
1687	serpin b12. [source:swissprot;acc:q96p63]	5767.69	6165.87	1.06904	
1688	megsin (tp55) (serpin b7). [source:swissprot;acc:o75635]	5767.69	6165.87	1.06904	
1689	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	5767.69	6165.87	1.06904	
1690	oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [source:swissprot;acc:p55055]	5767.69	6165.87	1.06904	
1691	upf0183 protein. [source:swissprot;acc:q9bsu1]	5767.69	6165.87	1.06904	
1692	antithrombin-iii precursor (atiii) (pro0309). [source:swissprot;acc:p01008]	5767.69	6165.87	1.06904	
1693	translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q14232]	5767.69	6165.87	1.06904	
1694	squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [source:swissprot;acc:p29508]	5767.69	6165.87	1.06904	
1695	oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [source:swissprot;acc:q13133]	5767.69	6165.87	1.06904	
1696	wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [source:swissprot;acc:q9y6w5]	6304.22	6738.77	1.06893	
1697	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	6304.21	6738.77	1.06893	
1698	wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [source:swissprot;acc:q92558]	6304.22	6738.77	1.06893	
1699	rest corepressor. [source:refseq;acc:nm_015156]	6304.21	6738.77	1.06893	
1700	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]	6326.24	6762.27	1.06892	
1701	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]	6326.24	6762.27	1.06892	
1702	dynamin 1-like protein isoform 3; dynamin-like protein. [source:refseq;acc:nm_005690]	6326.24	6762.27	1.06892	
1703	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [source:refseq;acc:nm_002645]	6326.24	6762.27	1.06892	
1704	homeobox protein six1 (sine oculis homeobox homolog 1). [source:swissprot;acc:q15475]	5778.4	6176.13	1.06883	
1705	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q13144]	5369.43	5738.73	1.06878	
1706	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q9nr50]	5369.43	5738.73	1.06878	
1707	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [source:swissprot;acc:q9uq80]	5777.1	6174.15	1.06873	
1708	metaxin 2. [source:swissprot;acc:o75431]	7033.72	7516.77	1.06868	
1709	homeobox protein six2 (sine oculis homeobox homolog 2). [source:swissprot;acc:q9npc8]	5775.55	6171.79	1.06861	
1710	camp-dependent protein kinase type ii-alpha regulatory chain. [source:swissprot;acc:p13861]	5916.13	6321.77	1.06857	
1711	protein kinase pkx1 (ec 2.7.1.-). [source:swissprot;acc:p51817]	5917.22	6322.72	1.06853	
1712	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [source:swissprot;acc:p22612]	5917.23	6322.73	1.06853	
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	

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/