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 description Gene Hugo Network Comparison Type Value Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1558 to 1607 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    390 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] no value Squared 28895.6 35572.8 1.23108
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 Rooted 50.3345 45.6718 1.10209
    rw1 protein (fragment). [swissprot;acc:q92545] TMEM131 Measured 4533.74 5279.4 1.16447
    391 40s ribosomal protein s16. [swissprot;acc:p17008] RPS16 Ranked 241.828 263.62 1.09011
    importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] KPNB1 Squared 28895.6 35572.8 1.23108
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1 Rooted 50.3345 45.6718 1.10209
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP Measured 3658.76 3144.39 1.16358
    392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] RPL13A Ranked 241.83 263.615 1.09008
    60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L Rooted 50.3313 45.6913 1.10155
    atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] DDX54 Measured 3641.89 4236.95 1.16339
    transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] TBL1X Squared 28895.6 35572.8 1.23108
    393 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] POLR2A Rooted 49.8842 45.2875 1.1015
    eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] EIF4E Measured 4490.28 5222.25 1.16301
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A Ranked 225.719 207.072 1.09005
    transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] TBL1Y Squared 28895.6 35572.8 1.23108
    394 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] BAIAP3 Measured 4490.28 5222.25 1.16301
    dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] DPP9 Ranked 218.827 238.407 1.08948
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Squared 17248.4 21214 1.22991
    pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] CDC40 Rooted 58.6533 64.5958 1.10132
    395 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] DPP8 Ranked 218.827 238.407 1.08948
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 Squared 17254.4 21218.1 1.22972
    protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] EIF1 Rooted 50.0423 45.4523 1.10098
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Measured 4532.73 5269.33 1.16251
    396 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF Rooted 116.797 106.111 1.10071
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Squared 17256.5 21219.6 1.22966
    putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] no value Ranked 240.801 262.34 1.08945
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B Measured 6563.65 7627.29 1.16205
    397 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 Squared 17257.5 21220.3 1.22963
    nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] SNW1 Measured 5367.04 6233.12 1.16137
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 Rooted 116.792 106.107 1.1007
    t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] CCT3 Ranked 110.689 101.613 1.08932
    398 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] IMMP2L Squared 18929.1 23222.8 1.22683
    muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] ITGB1BP3 Ranked 218.818 238.358 1.0893
    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] PPP2R5E Rooted 116.707 106.044 1.10055
    xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] XAB2 Measured 5084.26 5904.1 1.16125
    399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] CLTC Ranked 207.889 226.226 1.08821
    cyclin g2. [swissprot;acc:q16589] CCNG2 Rooted 116.707 106.044 1.10055
    microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] no value Squared 18929.1 23222.8 1.22683
    neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] CHRNA7 Measured 5201.41 4479.76 1.16109
    400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] ADCY6
    cyclin g1 (cyclin g). [swissprot;acc:p51959] CCNG1 Rooted 116.707 106.044 1.10055
    glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] GYS1 Squared 39478.8 48419 1.22646
    phosducin-like protein (phlp). [swissprot;acc:q13371] PDCL Ranked 207.908 226.218 1.08807
    401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] ADCY5 Measured 5201.41 4479.76 1.16109
    axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] DNALI1 Squared 33044.3 40524.8 1.22638
    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] RPA1 Ranked 207.908 226.218 1.08807
    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] PPP2R5A Rooted 116.707 106.044 1.10055
    402 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] no value Squared 39472 48393.1 1.22601
    eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] EIF6 Rooted 50.1918 55.2294 1.10037
    leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] LRRC15 Measured 5201.41 4479.76 1.16109

    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/