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 [...,...].
    Gene Rank Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1701 to 1750 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    426 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Rooted 55.1073 60.5285 1.09838
    DCTN5 dynactin 4. [refseq;acc:nm_032486] Ranked 233.142 252.253 1.08197
    PEF1 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Measured 5942.49 6853.15 1.15325
    UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Squared 20267.8 24644.8 1.21596
    427 CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Rooted 54.4927 49.6125 1.09837
    PMS2 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Squared 25380.3 30835.9 1.21495
    POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Ranked 239.977 259.525 1.08146
    TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured 11736.6 13531.9 1.15297
    428 ADCY6 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Rooted 54.4927 49.6125 1.09837
    ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Squared 29101.9 35347 1.21459
    DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Ranked 253.852 234.808 1.0811
    GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Measured 3721.19 4288.17 1.15237
    429 ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Rooted 54.4927 49.6125 1.09837
    PDCD6 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Squared 29101.9 35347 1.21459
    POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Ranked 239.709 259.038 1.08064
    SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Measured 6272.91 7226.06 1.15195
    430 ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Squared 29098.8 35342.6 1.21457
    LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Rooted 54.4927 49.6125 1.09837
    LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Ranked 227.748 210.888 1.07995
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Measured 3804.09 4379.37 1.15123
    431 DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 3849.94 4431.36 1.15102
    FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Rooted 54.4927 49.6125 1.09837
    SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared 29096 35338.7 1.21456
    TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Ranked 236.245 255.113 1.07987
    432 CAPNS1 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Squared 29095.3 35337.6 1.21455
    ENDOG endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Ranked 212.547 229.411 1.07934
    LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Rooted 54.4927 49.6125 1.09837
    PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Measured 5244.71 6036.27 1.15093
    433 AIFM1 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Ranked 212.547 229.411 1.07934
    GCA grancalcin. [swissprot;acc:p28676] Squared 29095.7 35338.3 1.21455
    LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Rooted 54.4927 49.6125 1.09837
    PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Measured 5244.88 6036.38 1.15091
    434 SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Squared 18306.1 22230.6 1.21438
    SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted 54.4927 49.6125 1.09837
    TBX6 t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked 212.547 229.411 1.07934
    UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Measured 5246.38 6037.37 1.15077
    435 CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Squared 26598.9 32283.5 1.21372
    POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked 221.522 205.286 1.07909
    PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Measured 5233.86 6022.6 1.1507
    RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] Rooted 50.832 46.3081 1.09769
    436 CYB5R1 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Squared 26598.9 32283.5 1.21372
    PXN paxillin. [swissprot;acc:p49023] Ranked 221.522 205.286 1.07909
    SORBS2 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Measured 6230.94 7168.2 1.15042
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Rooted 210.928 192.165 1.09764
    437 CYB5R3 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Squared 26598.9 32283.5 1.21372
    PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Measured 3779.92 4348.48 1.15042
    TRIP10 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Ranked 209.921 226.459 1.07878
    ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Rooted 51.0466 56.024 1.09751
    438 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Ranked 233.723 216.674 1.07869
    ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Measured 6252.58 7192.88 1.15039

    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/