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 Network Comparison Type Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 6991 to 7040 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    437 TRIP10 Subtracted Ranked cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] High confidence 209.921 226.459 16.538
    ZNF593 Divided Rooted zinc finger protein t86. [swissprot;acc:o00488] 51.0466 56.024 1.09751
    438 no value Measured sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Low confidence 7591.67 7981.63 1.05137
    ARD1A Ranked n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] High confidence 233.723 216.674 1.07869
    ARID1A Measured swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 6252.58 7192.88 1.15039
    BAG3 Rooted bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 55.1867 60.5522 1.09722
    BOP1 Subtracted Ranked block of proliferation 1. [swissprot;acc:q14137] 250.794 234.433 16.361
    CUTL1 Rooted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Low confidence 73.1956 76.5683 3.3727
    E2F1 Measured transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] 6885.52 7293.37 407.85
    ELL Divided Ranked rna polymerase ii elongation factor ell (eleven-nineteen lysine-rich leukemia protein). [swissprot;acc:p55199] 198.572 205.504 1.03491
    GABRA4 Subtracted Rooted gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] High confidence 66.082 71.6525 5.5705
    GTPBP3 Squared mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Low confidence 54392.4 57394.7 3002.3
    MOCS2 Divided Rooted molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] 69.6417 72.8914 1.04666
    NDUFA6 Subtracted Measured nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] High confidence 6739.85 7644.63 904.78
    PRODH2 Squared kidney and liver proline oxidase 1. [refseq;acc:nm_021232] 28967 34626.4 5659.4
    SERPINB12 Divided serpin b12. [swissprot;acc:q96p63] Low confidence 49536.2 46463.8 1.06612
    SORBS2 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] High confidence 28863.2 35031.5 1.21371
    UTP14A Subtracted Ranked serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Low confidence 206.703 199.782 6.921
    439 no value Divided Measured ectonucleoside triphosphate diphosphohydrolase 6 (ec 3.6.1.6) (ntpdase6) (cd39 antigen-like 2). [swissprot;acc:o75354] 8886.95 9342.85 1.0513
    Rooted dok-like protein. [refseq;acc:nm_024872] High confidence 63.2134 69.352 1.09711
    ARRB1 Ranked beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Low confidence 194.237 187.689 1.03489
    ATRIP Rooted three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166] 68.6483 71.8511 1.04666
    CDC23 Squared cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] High confidence 51616.7 42588.9 1.21198
    E2F2 Subtracted Measured transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Low confidence 6885.52 7293.37 407.85
    GABRE Rooted gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] High confidence 66.082 71.6525 5.5705
    JMJD2B Ranked f16601_1, partial cds (fragment). [sptrembl;acc:o75274] Low confidence 206.703 199.782 6.921
    PCSK7 Squared proprotein convertase subtilisin/kexin type 7 precursor (ec 3.4.21.-) (proprotein convertase pc7) (subtilisin/kexin-like protease pc7) (prohormone convertase pc7) (pc8) (hpc8) (lymphoma proprotein convertase). [swissprot;acc:q16549] 49247 46248 2999
    PDCD6 Divided Measured programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] High confidence 6252.58 7192.88 1.15039
    PDK1 Subtracted Rooted [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Low confidence 71.1071 74.4797 3.3726
    PDXDC1 Measured similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] High confidence 6739.85 7644.63 904.78
    PES1 Ranked pescadillo homolog 1. [swissprot;acc:o00541] 251.297 234.941 16.356
    RPS9 Divided 40s ribosomal protein s9. [swissprot;acc:p46781] 238.986 257.784 1.07866
    SERPINB7 Squared megsin (tp55) (serpin b7). [swissprot;acc:o75635] Low confidence 49536.2 46463.8 1.06612
    SLC5A5 Subtracted sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] High confidence 28937.1 34588.8 5651.7
    440 no value Divided dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 26348.4 31925.8 1.21168
    hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Low confidence 49536.2 46463.8 1.06612
    Subtracted Measured small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 8727.92 9135.42 407.5
    Ranked 40s ribosomal protein s26. [swissprot;acc:p02383] High confidence 210.224 226.578 16.354
    CAPNS1 Divided Measured calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 6251.91 7192.08 1.15038
    CUTL2 Subtracted Rooted homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Low confidence 73.198 76.5693 3.3713
    CYP4X1 Divided Ranked likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 203.045 196.204 1.03487
    DOK2 Rooted docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] High confidence 63.2134 69.352 1.09711
    FOXP3 Measured forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Low confidence 6368.6 6694.68 1.0512
    GABRA1 Subtracted Rooted gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] High confidence 66.082 71.6525 5.5705
    HOXD9 Measured homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 6740.5 7644.76 904.26
    IDE Squared insulin-degrading enzyme (ec 3.4.24.56) (insulysin) (insulinase) (insulin protease). [swissprot;acc:p14735] Low confidence 49247 46248 2999
    JMJD2C Ranked gene amplified in squamous cell carcinoma 1. [refseq;acc:nm_015061] 206.703 199.782 6.921
    MOCS3 Divided Rooted molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] 69.6417 72.8914 1.04666
    NDC80 Ranked highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] High confidence 231.802 249.983 1.07843
    PEF1 Subtracted Squared pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 27096.7 32743.5 5646.8

    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/