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 Hugo description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 3658 to 3707 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    1829 EXOC3 exocyst complex component sec6. [swissprot;acc:o60645] Low confidence 194.831 191.012 1.01999
    1830 no value similar to phosphatidylinositol 4-kinase, catalytic, alpha polypeptide. [sptrembl;acc:q8wuk7] 200.699 196.767 1.01998
    PFKM 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] High confidence 240.32 243.069 1.01144
    1831 no value f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 214.746 212.328 1.01139
    glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Low confidence 200.759 196.827 1.01998
    1832 PSMD6 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] 200.092 196.175 1.01997
    SLC4A1AP solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] High confidence 180.409 182.459 1.01136
    1833 CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
    NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Low confidence 202.814 198.844 1.01997
    1834 CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] High confidence 180.409 182.459 1.01136
    TRMT11 mds024 protein. [refseq;acc:nm_021820] Low confidence 202.243 198.284 1.01997
    1835 no value protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 200.267 196.347 1.01996
    GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] High confidence 194.573 192.396 1.01132
    1836 ENOPH1 e-1 enzyme. [refseq;acc:nm_021204] Low confidence 199.38 195.479 1.01996
    RPIA ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] High confidence 208.821 211.17 1.01125
    1837 DDX52 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Low confidence 205.024 201.012 1.01996
    KHK ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] High confidence 218.984 221.446 1.01124
    1838 no value purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
    LRRC4 nag14 protein. [refseq;acc:nm_022143] Low confidence 200.267 196.347 1.01996
    1839 EIF2S2 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] High confidence 221.525 224.001 1.01118
    MGLL monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Low confidence 198.876 194.985 1.01996
    1840 APEX1 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] High confidence 211.882 209.544 1.01116
    PET112L probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Low confidence 200.397 196.475 1.01996
    1841 no value dom-3 homolog z isoform 2. [refseq;acc:nm_005510] 201.124 197.192 1.01994
    PARL presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] High confidence 212.455 210.113 1.01115
    1842 no value ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Low confidence 201.804 197.86 1.01993
    BBOX1 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] High confidence 212.455 210.113 1.01115
    1843 ATP11A potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]
    NAT5 n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Low confidence 201.16 197.23 1.01993
    1844 LIAS lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] 200.522 196.605 1.01992
    PAX6 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] High confidence 214.773 212.417 1.01109
    1845 ABI2 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] 217.077 214.702 1.01106
    CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Low confidence 197.771 193.908 1.01992
    1846 ABI1 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] High confidence 217.066 214.698 1.01103
    CAMKK2 calcium/calmodulin-dependent protein kinase kinase 2 beta isoform 1; camkk beta protein; calcium/calmodulin-dependent protein kinase beta. [refseq;acc:nm_006549] Low confidence 201.365 197.433 1.01992
    1847 no value brain protein 16. [refseq;acc:nm_016458] High confidence 216.811 219.195 1.011
    CBX1 chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] Low confidence 202.264 198.314 1.01992
    1848 BAAT bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] High confidence 218.441 216.064 1.011
    GRWD1 glutamate-rich wd-repeat protein. [swissprot;acc:q9bq67] Low confidence 203.397 199.424 1.01992
    1849 ACOT1 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] High confidence 218.445 216.074 1.01097
    BTAF1 tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] Low confidence 203.397 199.424 1.01992
    1850 CAMKK1 calcium/calmodulin-dependent protein kinase 1 alpha isoform a; camkk alpha protein. [refseq;acc:nm_032294] 201.365 197.433
    CAP1 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] High confidence 215.931 213.587 1.01097
    1851 ACOT4 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 218.448 216.08 1.01096
    ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Low confidence 203.171 199.205 1.01991
    1852 no value 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] High confidence 196.008 198.154 1.01095
    GTPBP2 gtp binding protein 2. [refseq;acc:nm_019096] Low confidence 203.096 199.132 1.01991
    1853 CREBL1 cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]
    TTL tubulin-tyrosine ligase. [refseq;acc:nm_153712] High confidence 217.924 215.564 1.01095
    1854 EIF2B5 translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] 222.215 224.637 1.0109

    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/