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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1808 to 1857 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1808 ral-a exchange factor ralgps2. [refseq;acc:nm_152663] RALGPS2 211.102 208.651 1.01175
    1809 stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] STUB1
    1810 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] no value 223.214 225.827 1.01171
    1811 polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] GALNT2 216.854 214.35 1.01168
    1812 cyclin c. [swissprot;acc:p24863] CCNC 217.071 214.564
    1813 similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] GALNTL1 216.854 214.35
    1814 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] PPP1CC 122.3 123.727 1.01167
    1815 dpy-30-like protein. [swissprot;acc:q9c005] no value 220.462 217.926 1.01164
    1816 rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] RAB11FIP1
    1817 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] RAB11FIP5
    1818 neighbor of cox4. [swissprot;acc:o43402] COX4NB
    1819 protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] C14orf122
    1820 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] ATP9A
    1821 rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] RBM38 218.36 215.874 1.01152
    1822 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] PFKL 240.32 243.085 1.01151
    1823 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] FXR2 202.386 200.086 1.0115
    1824 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] CAPZA1 214.722 212.281
    1825 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] FXR1 202.386 200.086
    1826 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] NUP43 202.393 200.094 1.01149
    1827 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] NME3 191.39 189.219 1.01147
    1828 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] FMR1 202.41 200.115
    1829 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] CAD 212.884 215.323 1.01146
    1830 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] PFKM 240.32 243.069 1.01144
    1831 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] no value 214.746 212.328 1.01139
    1832 solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] SLC4A1AP 180.409 182.459 1.01136
    1833 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] CKS2
    1834 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] CTNNAL1
    1835 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] GORASP2 194.573 192.396 1.01132
    1836 ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] RPIA 208.821 211.17 1.01125
    1837 ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] KHK 218.984 221.446 1.01124
    1838 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] no value
    1839 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] EIF2S2 221.525 224.001 1.01118
    1840 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] APEX1 211.882 209.544 1.01116
    1841 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] PARL 212.455 210.113 1.01115
    1842 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] BBOX1
    1843 potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] ATP11A
    1844 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] PAX6 214.773 212.417 1.01109
    1845 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] ABI2 217.077 214.702 1.01106
    1846 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] ABI1 217.066 214.698 1.01103
    1847 brain protein 16. [refseq;acc:nm_016458] no value 216.811 219.195 1.011
    1848 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] BAAT 218.441 216.064
    1849 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] ACOT1 218.445 216.074 1.01097
    1850 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] CAP1 215.931 213.587
    1851 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] ACOT4 218.448 216.08 1.01096
    1852 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] no value 196.008 198.154 1.01095
    1853 tubulin-tyrosine ligase. [refseq;acc:nm_153712] TTL 217.924 215.564
    1854 translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] EIF2B5 222.215 224.637 1.0109
    1855 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] GRSF1 217.891 215.542
    1856 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] HNRPH3 217.892 215.543
    1857 translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] EIF2B3 222.215 224.637

    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
    - Hugo is the HGNC identifier if it exists
    - 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/