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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1701 to 1750 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		green
    		network_comparison
    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] 6326.24 6762.27 1.06892
    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
    1750 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] 5384.89 5746.51 1.06715

    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/