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 [...,...].
    Filtered Rank Gene Hugo description Value Type Network Comparison Type Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
    Filtered  : 0
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    1 ARFGAP3 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 4294 15915 3.70633
    STARD3 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 5865 14977 2.55362
    2 no value mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 21883 2.45711
    STARD3 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 5865 14977 2.55362
    3 no value nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 11083.9 2.47638
    NOTCH1 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Low confidence 9607 20617 2.14604
    4 no value mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 8906 21883 2.45711
    NOTCH2 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Low confidence 9607 20617 2.14604
    5 no value ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] High confidence 5510.5 11965.7 2.17144
    UTY ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 10889.4 19873 1.82499
    6 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] 5575.71 9583.37 1.71877
    UBE3B ubiquitin protein ligase. [refseq;acc:nm_130466] High confidence 7523 15339.2 2.03897
    7 no value fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Low confidence 11543 6812 1.69451
    PERLD1 cab2. [refseq;acc:nm_033419] High confidence 21866 10950 1.99689
    8 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 22286 13216 1.68629
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 11525 21888 1.89918
    9 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 22286 13216 1.68629
    TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 11525 21888 1.89918
    10 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 22286 13216 1.68629
    FBP2 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] High confidence 7509.39 14178.1 1.88805
    11 no value ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Low confidence 13730.5 8257 1.66289
    ATP9A potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] High confidence 11627 6248 1.86092
    12 no value anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Low confidence 3190 1933 1.65028
    FPGS folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] High confidence 9429.18 5208.84 1.81023
    13 no value heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 5210.5 9264.5 1.77804
    SORD sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Low confidence 7435.56 12191.6 1.63963
    14 no value dystrophin. [swissprot;acc:p11532] High confidence 10232.5 18054.8 1.76446
    ptd016 protein. [refseq;acc:nm_016125] Low confidence 18050 11234 1.60673
    15 succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] High confidence 19403 11267 1.72211
    APC2 adenomatous polyposis coli like. [refseq;acc:nm_005883] Low confidence 12074.1 7597.61 1.5892
    16 no value beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 7395 11625 1.57201
    CCNH cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] High confidence 12170.7 20670.6 1.69839
    17 no value fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 11543 6812 1.69451
    LRRFIP1 leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Low confidence 8082.33 5266.67 1.53462
    18 no value early hematopoietic zinc finger. [refseq;acc:nm_015461] 5850.23 8903.28 1.52187
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence 22286 13216 1.68629
    19 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 3208.8 4871.6 1.5182
    20 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 22286 13216 1.68629
    GNB1L guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] Low confidence 22422 14964 1.4984
    21 no value dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 3859 2582 1.49458
    ACRC acrc protein; putative nuclear protein. [refseq;acc:nm_052957] High confidence 6313.38 10621.4 1.68236
    22 CTSZ cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Low confidence 11515 7867 1.46371
    PNPO pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 20989 12479 1.68195
    23 HGS hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 15520.4 9285.44 1.67148
    SERPINB12 serpin b12. [swissprot;acc:q96p63] Low confidence 14604.2 21138.6 1.44743
    24 no value ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] High confidence 13730.5 8257 1.66289
    hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Low confidence 14592 21113.7 1.44694
    25 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 13730.5 8257 1.66289
    NDUFA5 nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Low confidence 9830 6909 1.42278

    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/