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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1358 to 1407 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    hskin17 protein. [refseq;acc:nm_012311] 1697 KIN 217.624 214.69 1.01367
    hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 2258 CDC37 223.888 225.191 1.00582
    human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 1486 HIVEP3 207.877 203.989 1.01906
    human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] 1488 HIVEP2
    huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 1995 HIP1 188.961 190.73 1.00936
    huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 1993 HIP1R 189.052 190.835 1.00943
    huntingtin interacting protein c. [refseq;acc:nm_012272] 195 PRPF40B 227.971 200.417 1.13748
    huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 729 no value 208.874 219.708 1.05187
    huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 949 217.253 209.826 1.0354
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 179 226.884 194.79 1.16476
    hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 2415 218.2 218.984 1.00359
    hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] 2191 HUS1 209.54 208.162 1.00662
    hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282] 2192 HABP4
    hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] 1294 HAS1 221.093 226.399 1.024
    hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] 1291 HAS2
    hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] 1295 HAS3
    hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] 1104 HAO1 231.922 238.486 1.0283
    hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 916 HAO2 232.512 241.288 1.03774
    hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] 1640 HAGH 194.516 197.364 1.01464
    hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 1648 no value 219.745 222.928 1.01448
    hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] 2304 HMGCS1 191.567 192.542 1.00509
    hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] 2302 HMGCS2
    hyporthetical protein mgc27169. [refseq;acc:nm_176782] 1782 C1orf179 206.332 203.874 1.01206
    hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 852 HPRT1 193.114 185.412 1.04154
    hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] 674 HIF3A 226.497 214.355 1.05664
    i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] 1162 NKIRAS2 220.758 215.097 1.02632
    immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 1888 ICT1 218.414 216.131 1.01056
    immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] 1706 IGBP1 223.846 220.847 1.01358
    imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 926 IMMP2L 217.942 210.139 1.03713
    importin 4. [refseq;acc:nm_024658] 2356 no value 220.921 221.863 1.00426
    importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 2709 220.521 220.395 1.00057
    importin 8; ran-binding protein 8. [refseq;acc:nm_006390] 2710 IPO8
    importin 9. [refseq;acc:nm_018085] 2860 no value 0.00001 0.00001 1
    importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 1952 KPNA1 211.647 213.724 1.00981
    importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 2780 KPNA2 0.00001 0.00001 1
    importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 1018 KPNA3 217.361 210.554 1.03233
    importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 1016 KPNA4 217.369 210.561
    importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 1970 KPNA6 211.62 213.683 1.00975
    importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] 2523 KPNB1 201.96 201.488 1.00234
    importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] 1676 TNPO1 218.691 215.645 1.01413
    importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] 1474 RANBP5 218.582 214.427 1.01938
    importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 1459 CSE1L 192.336 188.637 1.01961
    indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] 2225 INMT 221.509 220.108 1.00637
    inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] 806 GPR84 212.386 221.785 1.04425
    inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 500 ING2 224.662 240.673 1.07127
    inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] 506 ING1 224.535 240.476 1.071
    inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 1154 PPA1 224.307 230.242 1.02646
    inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] 1155 PPA2
    inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] 1695 IMPDH1 218.937 215.971 1.01373
    inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 1693 IMPDH2

    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/