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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1562 to 1611 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    391 RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] Ranked 241.828 263.62 1.09011
    SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Rooted 50.3345 45.6718 1.10209
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Measured 3658.76 3144.39 1.16358
    392 DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 3641.89 4236.95 1.16339
    RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Ranked 241.83 263.615 1.09008
    RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Rooted 50.3313 45.6913 1.10155
    TBL1X transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Squared 28895.6 35572.8 1.23108
    393 EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Measured 4490.28 5222.25 1.16301
    POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Rooted 49.8842 45.2875 1.1015
    TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Squared 28895.6 35572.8 1.23108
    TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Ranked 225.719 207.072 1.09005
    394 BAIAP3 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Measured 4490.28 5222.25 1.16301
    CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Rooted 58.6533 64.5958 1.10132
    DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Ranked 218.827 238.407 1.08948
    MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Squared 17248.4 21214 1.22991
    395 DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Ranked 218.827 238.407 1.08948
    EIF1 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Rooted 50.0423 45.4523 1.10098
    MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Squared 17254.4 21218.1 1.22972
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Measured 4532.73 5269.33 1.16251
    396 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Ranked 240.801 262.34 1.08945
    ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Rooted 116.797 106.111 1.10071
    MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Squared 17256.5 21219.6 1.22966
    RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Measured 6563.65 7627.29 1.16205
    397 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Ranked 110.689 101.613 1.08932
    RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Squared 17257.5 21220.3 1.22963
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Rooted 116.792 106.107 1.1007
    SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Measured 5367.04 6233.12 1.16137
    398 IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Squared 18929.1 23222.8 1.22683
    ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked 218.818 238.358 1.0893
    PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Rooted 116.707 106.044 1.10055
    XAB2 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Measured 5084.26 5904.1 1.16125
    399 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Squared 18929.1 23222.8 1.22683
    CCNG2 cyclin g2. [swissprot;acc:q16589] Rooted 116.707 106.044 1.10055
    CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Measured 5201.41 4479.76 1.16109
    CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Ranked 207.889 226.226 1.08821
    400 ADCY6 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Measured 5201.41 4479.76 1.16109
    CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] Rooted 116.707 106.044 1.10055
    GYS1 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Squared 39478.8 48419 1.22646
    PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] Ranked 207.908 226.218 1.08807
    401 ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured 5201.41 4479.76 1.16109
    DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Squared 33044.3 40524.8 1.22638
    PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Rooted 116.707 106.044 1.10055
    RPA1 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Ranked 207.908 226.218 1.08807
    402 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared 39472 48393.1 1.22601
    EIF6 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 55.2294 1.10037
    LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured 5201.41 4479.76 1.16109
    RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked 207.908 226.218 1.08807
    403 FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured 5201.41 4479.76 1.16109
    GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 48362.1 1.22548
    NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted 59.6834 65.6741 1.10037

    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/