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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1675 to 1724 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    419 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] CDC5L Measured 5493.1 6350.19 1.15603
    low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] FCER2 Ranked 233.539 253.197 1.08417
    420 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] RPL24 Squared 30924.3 37652.3 1.21756
    cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] CD209 Ranked 233.539 253.197 1.08417
    dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] POLE Rooted 51.7959 56.9253 1.09903
    hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] HPRT1 Measured 10235.2 11830.8 1.15589
    421 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] no value Rooted 50.4666 45.9317 1.09873
    cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL Squared 36933 44953.6 1.21717
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 Ranked 223.202 205.9 1.08403
    vav-2 protein. [swissprot;acc:p52735] VAV2 Measured 6660.02 7697.78 1.15582
    422 60s ribosomal protein l5. [swissprot;acc:p46777] RPL5 Rooted 50.4641 45.9293 1.09873
    dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] MLH3 Squared 25860 31475.4 1.21715
    nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] NXF5 Measured 5206.9 6010.04 1.15425
    ras-related protein rab-37. [swissprot;acc:q96ax2] RAB37 Ranked 240.287 260.193 1.08284
    423 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] CDH1 Rooted 50.4663 45.9313 1.09873
    nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] NXF3 Measured 5207.03 6010.1 1.15423
    ras-related protein rab-26. [swissprot;acc:q9ulw5] RAB26 Ranked 240.287 260.193 1.08284
    signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB Squared 36735.7 44689.6 1.21652
    424 60s ribosomal protein l23a. [swissprot;acc:p29316] no value Rooted 50.4703 45.9373 1.09868
    dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] POLR2C Ranked 240.287 260.193 1.08284
    mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] PMPCA Squared 20259.5 24635.7 1.21601
    nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] NXF1 Measured 5207.78 6010.45 1.15413
    425 40s ribosomal protein s20. [swissprot;acc:p17075] RPS20 Rooted 50.0161 45.5318 1.09849
    max protein. [swissprot;acc:p25912] MAX Ranked 227.828 210.561 1.082
    mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] PMPCB Squared 20258.6 24634.7 1.21601
    saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] NIP7 Measured 3729.02 4301.58 1.15354
    426 dynactin 4. [refseq;acc:nm_032486] DCTN5 Ranked 233.142 252.253 1.08197
    n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] ARD1A Rooted 55.1073 60.5285 1.09838
    pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] PEF1 Measured 5942.49 6853.15 1.15325
    ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] UQCRC1 Squared 20267.8 24644.8 1.21596
    427 dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] POLR2E Ranked 239.977 259.525 1.08146
    neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] CHRNA7 Rooted 54.4927 49.6125 1.09837
    pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] PMS2 Squared 25380.3 30835.9 1.21495
    trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] TRMU Measured 11736.6 13531.9 1.15297
    428 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] ADCY6 Rooted 54.4927 49.6125 1.09837
    atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] DDX54 Ranked 253.852 234.808 1.0811
    nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] GTPBP4 Measured 3721.19 4288.17 1.15237
    swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] ARID1A Squared 29101.9 35347 1.21459
    429 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] ADCY5 Rooted 54.4927 49.6125 1.09837
    polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] POLR3G Ranked 239.709 259.038 1.08064
    programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] PDCD6 Squared 29101.9 35347 1.21459
    vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] SORBS3 Measured 6272.91 7226.06 1.15195
    430 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] ARID1B Squared 29098.8 35342.6 1.21457
    leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] LRRC15 Rooted 54.4927 49.6125 1.09837
    transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] TFDP2 Measured 3804.09 4379.37 1.15123
    u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] LSM5 Ranked 227.748 210.888 1.07995
    431 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] DDX31 Measured 3849.94 4431.36 1.15102
    fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] FEM1B Rooted 54.4927 49.6125 1.09837
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] SRI Squared 29096 35338.7 1.21456
    trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] TRUB1 Ranked 236.245 255.113 1.07987

    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/