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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2808 to 2857 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 2552 CDY1B 193.12 193.467 1.0018
    testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 612 HIST1H2BA 247.47 233.441 1.0601
    testis-specific protein tex28. [swissprot;acc:o15482] 802 TEX28P2 212.386 221.785 1.04425
    testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 3021 CRISP2 0.00001 0.00001 1
    tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 855 CLEC3B 178.514 171.42 1.04138
    tetratricopeptide repeat protein 1 (tpr repeat protein 1). [swissprot;acc:q99614] 3060 TTC1 0.00001 0.00001 1
    tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] 2321 no value 203.909 202.925 1.00485
    tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] 1747 ERCC2 188.452 190.845 1.0127
    tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 410 no value 233.376 253.539 1.0864
    tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 411 GTF2H1
    tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 652 no value 248.994 235.255 1.0584
    tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] 1360 TGFBR1 223.89 228.805 1.02195
    thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] 2264 no value 221.599 220.351 1.00566
    thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] 900 TXN 229.171 238.048 1.03874
    thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755] 2666 TXNDC1 210.136 209.911 1.00107
    thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] 899 TXNDC2 229.171 238.048 1.03874
    thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] 2405 TXNIP 221.677 222.489 1.00366
    thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757] 2383 TXN2 212.724 213.574 1.004
    thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] 1037 GLRX3 228.412 235.609 1.03151
    thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 1024 TST 205.632 199.266 1.03195
    thousand and one amino acid protein kinase. [refseq;acc:nm_004783] 2906 TAOK2 0.00001 0.00001 1
    thrombospondin 3 precursor. [swissprot;acc:p49746] 227 THBS3 239.99 269.234 1.12186
    thymic stromal co-transporter. [refseq;acc:nm_033051] 472 SLC46A2 248.152 267.226 1.07686
    thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142] 2837 TK2 0.00001 0.00001 1
    thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] 2104 DTYMK 209.328 207.813 1.00729
    thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] 1590 TYMS 225.119 228.769 1.01621
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 2703 PRSS16 188.435 188.311 1.00066
    thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 1460 TRIP12 205.817 209.851 1.0196
    thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] 1621 ZNHIT3 228.611 225.185 1.01521
    tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 2816 TIGD1 0.00001 0.00001 1
    tigger transposable element derived 6. [refseq;acc:nm_030953] 2853 TIGD6
    tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 2944 TIGD7
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 133 TOB1 350 290 1.2069
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 132 TOB2
    toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] 2540 TLR2 217.144 216.699 1.00205
    topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] 2642 TOPBP1 194.097 194.328 1.00119
    topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] 2073 PAPD5 229.267 227.433 1.00806
    trabid protein. [swissprot;acc:q9ugi0] 3210 ZRANB1 0.00001 0.00001 1
    traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] 2031 TTRAP 218.466 216.562 1.00879
    trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 2322 PDSS1 236.023 234.905 1.00476
    transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] 2364 TALDO1 212.816 213.697 1.00414
    transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 1619 no value 227.768 231.246 1.01527
    transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] 1618 TCEA2
    transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [swissprot;acc:q99081] 2948 TCF12 0.00001 0.00001 1
    transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 2940 no value
    transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] 2279 ZEB1 191.936 190.909 1.00538
    transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] 2969 TFAP2A 0.00001 0.00001 1
    transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481] 3220 TFAP2B
    transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754] 3164 TFAP2C
    transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 865 BTF3 211.961 203.814 1.03997

    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/