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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Network Comparison Type Gene Value Type Rank Interaction Map network_comparison description red green Filtered
Results: HTML CSV LaTeX Showing element 1700 to 1749 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
network_comparison
description
red
green
1700 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). [swissprot;acc:o75747] 6326.24 6762.27
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 1.06883 homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] 5778.4 6176.13
1705 1.06878 translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] 5369.43 5738.73
1706 translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50]
1707 1.06873 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] 5777.1 6174.15
1708 1.06868 metaxin 2. [swissprot;acc:o75431] 7033.72 7516.77
1709 1.06861 homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] 5775.55 6171.79
1710 1.06857 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 5916.13 6321.77
1711 1.06853 protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] 5917.22 6322.72
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 1.06849 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 5918.48 6323.83
1716 1.06844 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
1717 1.06842 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
1718 1.06831 coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] 9720.64 9099.1
1719 1.06827 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 5458.12 5830.76
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 1.06818 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
1726 1.0679 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
1727 1.06783 phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 6260.43 6685.05
1728 1.06782 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 5475.44 5127.66
1729 phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 6259.8 6684.31
1730 1.06781 phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] 6684.3
1731 1.06776 lamin b2. [swissprot;acc:q03252] 5840.77 6236.53
1732 1.06768 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
1733 1.06765 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
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 1.06763 twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] 5925.65 6326.43
1737 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]
1738 1.06761 ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 5885.08 6282.97
1739 1.06743 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] 5695.57 6079.61
1740 1.06738 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] 5878.2 6274.27
1741 1.06734 serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] 6297.05 6721.08
1742 1.06729 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
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 1.06728 regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] 5683.17 6065.55
1747 1.06724 cerebral cell adhesion molecule. [refseq;acc:nm_016174] 9596.59 10241.9
1748 1.06723 doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] 6301.03 6724.63
1749 1.06721 electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 7919.76 8452.01

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.
- http://analysis.yellowcouch.org/