MK5 Microarray Data

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

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Showing element 1680 to 1729 of 3228 in total

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

Rank	description	red	green	network_comparison
1680	methylenetetrahydrofolate reductase (ec 1.5.1.20). [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). [swissprot;acc:q96kx2]	6304.74	6740.66	1.06914
1682	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
1683	ring finger protein 20. [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. [refseq;acc:nm_014771]
1685	gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6]	6088.07	6508.45	1.06905
1686	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603]
1687	serpin b12. [swissprot;acc:q96p63]	5767.69	6165.87	1.06904
1688	megsin (tp55) (serpin b7). [swissprot;acc:o75635]
1689	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
1690	oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]
1691	upf0183 protein. [swissprot;acc:q9bsu1]
1692	antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
1693	translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232]
1694	squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508]
1695	oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133]
1696	wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [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). [swissprot;acc:q9upy6]	6304.21
1698	wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]	6304.22
1699	rest corepressor. [refseq;acc:nm_015156]	6304.21
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). [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). [swissprot;acc:o00750]
1702	dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]
1703	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645]
1704	homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475]	5778.4	6176.13	1.06883
1705	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144]	5369.43	5738.73	1.06878
1706	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50]
1707	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80]	5777.1	6174.15	1.06873
1708	metaxin 2. [swissprot;acc:o75431]	7033.72	7516.77	1.06868
1709	homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8]	5775.55	6171.79	1.06861
1710	camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861]	5916.13	6321.77	1.06857
1711	protein kinase pkx1 (ec 2.7.1.-). [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). [swissprot;acc:p22612]	5917.23	6322.73
1713	camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694]
1714	camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612]
1715	camp-dependent protein kinase type ii-beta regulatory chain. [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). [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). [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]. [swissprot;acc:p53621]	9720.64	9099.1	1.06831
1719	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949]	5458.12	5830.76	1.06827
1720	putative ankyrin-repeat containing protein. [refseq;acc:nm_025185]
1721	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]
1722	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8]
1723	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]
1724	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]
1725	glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [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). [swissprot;acc:o75521]	7048.79	7527.42	1.0679
1727	phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7]	6260.43	6685.05	1.06783
1728	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	5475.44	5127.66	1.06782
1729	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	6259.8	6684.31

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.