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 1700 to 1749 of 3228 in total

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

Rank	description	red	green	network_comparison
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
1730	phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2]		6684.3	1.06781
1731	lamin b2. [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). [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). [swissprot;acc:p04720]	5874.83	6272.26	1.06765
1734	zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312]
1735	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
1736	twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830]	5925.65	6326.43	1.06763
1737	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]
1738	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	5885.08	6282.97	1.06761
1739	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [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). [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). [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. [refseq;acc:nm_014268]	6298.76	6722.61	1.06729
1743	histidine-rich membrane protein ke4. [swissprot;acc:q92504]	6298.81	6722.65
1744	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]
1745	microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]	6298.77	6722.62
1746	regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127]	5683.17	6065.55	1.06728
1747	cerebral cell adhesion molecule. [refseq;acc:nm_016174]	9596.59	10241.9	1.06724
1748	doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	6301.03	6724.63	1.06723
1749	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	7919.76	8452.01	1.06721

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.