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 Value Type description 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
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    419 FCER2 Ranked low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 233.539 253.197 1.08417
    GSTO2 Rooted ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 55.5489 50.535 1.09922
    420 CD209 Ranked cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 233.539 253.197 1.08417
    HPRT1 Measured hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 10235.2 11830.8 1.15589
    POLE Rooted dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 51.7959 56.9253 1.09903
    RPL24 Squared 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 30924.3 37652.3 1.21756
    421 no value Rooted c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 50.4666 45.9317 1.09873
    CBL Squared cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 36933 44953.6 1.21717
    TFIP11 Ranked tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 223.202 205.9 1.08403
    VAV2 Measured vav-2 protein. [swissprot;acc:p52735] 6660.02 7697.78 1.15582
    422 MLH3 Squared dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 25860 31475.4 1.21715
    NXF5 Measured nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 5206.9 6010.04 1.15425
    RAB37 Ranked ras-related protein rab-37. [swissprot;acc:q96ax2] 240.287 260.193 1.08284
    RPL5 Rooted 60s ribosomal protein l5. [swissprot;acc:p46777] 50.4641 45.9293 1.09873
    423 CBLB Squared signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 36735.7 44689.6 1.21652
    CDH1 Rooted epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 50.4663 45.9313 1.09873
    NXF3 Measured nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 5207.03 6010.1 1.15423
    RAB26 Ranked ras-related protein rab-26. [swissprot;acc:q9ulw5] 240.287 260.193 1.08284
    424 no value Rooted 60s ribosomal protein l23a. [swissprot;acc:p29316] 50.4703 45.9373 1.09868
    NXF1 Measured nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 5207.78 6010.45 1.15413
    PMPCA Squared mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 20259.5 24635.7 1.21601
    POLR2C Ranked dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 240.287 260.193 1.08284
    425 MAX max protein. [swissprot;acc:p25912] 227.828 210.561 1.082
    NIP7 Measured saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 3729.02 4301.58 1.15354
    PMPCB Squared mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 20258.6 24634.7 1.21601
    RPS20 Rooted 40s ribosomal protein s20. [swissprot;acc:p17075] 50.0161 45.5318 1.09849
    426 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 55.1073 60.5285 1.09838
    DCTN5 Ranked dynactin 4. [refseq;acc:nm_032486] 233.142 252.253 1.08197
    PEF1 Measured pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 5942.49 6853.15 1.15325
    UQCRC1 Squared ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 20267.8 24644.8 1.21596
    427 CHRNA7 Rooted neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 54.4927 49.6125 1.09837
    PMS2 Squared pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 25380.3 30835.9 1.21495
    POLR2E Ranked dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 239.977 259.525 1.08146
    TRMU Measured trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 11736.6 13531.9 1.15297
    428 ADCY6 Rooted adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 54.4927 49.6125 1.09837
    ARID1A Squared swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 29101.9 35347 1.21459
    DDX54 Ranked atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 253.852 234.808 1.0811
    GTPBP4 Measured nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 3721.19 4288.17 1.15237
    429 ADCY5 Rooted adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 54.4927 49.6125 1.09837
    PDCD6 Squared programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 29101.9 35347 1.21459
    POLR3G Ranked polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 239.709 259.038 1.08064
    SORBS3 Measured vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 6272.91 7226.06 1.15195
    430 ARID1B Squared brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 29098.8 35342.6 1.21457
    LRRC15 Rooted leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 54.4927 49.6125 1.09837
    LSM5 Ranked u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 227.748 210.888 1.07995
    TFDP2 Measured transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 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 Rooted fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 54.4927 49.6125 1.09837
    SRI Squared sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 29096 35338.7 1.21456
    TRUB1 Ranked trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 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/