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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3258 to 3307 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    815 EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Subtracted High confidence 246.354 237.223 9.131
    NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Divided Low confidence 203.907 198.706 1.02617
    STX1B syntaxin 1b. [swissprot;acc:q15531] High confidence 212.386 221.785 1.04425
    816 CDC25A m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Low confidence 207.541 202.25 1.02616
    EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Subtracted High confidence 246.354 237.223 9.131
    MRPL28 melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Divided 212.386 221.785 1.04425
    TMLHE trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Subtracted Low confidence 204.064 198.895 5.169
    817 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] High confidence 110.689 101.613 9.076
    GABBR2 gamma-aminobutyric acid type b receptor, subunit 2 precursor (gaba-b receptor 2) (gaba-b-r2) (gb2) (gababr2) (g protein-coupled receptor 51) (gpr 51) (hg20). [swissprot;acc:o75899] Low confidence 204.064 198.895 5.169
    LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Divided 202.15 197.002 1.02613
    RFXANK dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] High confidence 212.386 221.785 1.04425
    818 no value 60s ribosomal protein l39. [swissprot;acc:p02404] Subtracted 234.025 224.958 9.067
    ERAL1 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Low confidence 204.064 198.895 5.169
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided High confidence 168.592 161.452 1.04422
    SERHL2 serine hydrolase-like protein (ec 3.1.-.-). [swissprot;acc:q9h4i8] Low confidence 208.488 203.181 1.02612
    819 no value 60s ribosomal protein l18a. [swissprot;acc:q02543] Subtracted High confidence 234.025 224.958 9.067
    aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Divided Low confidence 208.488 203.181 1.02612
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted 149.423 144.256 5.167
    POLR2I dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Divided High confidence 228.563 238.668 1.04421
    820 ABLIM2 actin binding lim protein 2. [refseq;acc:nm_032432] Low confidence 208.488 203.181 1.02612
    FOXO1 forkhead box protein o1a (forkhead in rhabdomyosarcoma). [swissprot;acc:q12778] Subtracted 204.497 199.336 5.161
    MRPS2 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Divided High confidence 221.716 231.501 1.04413
    RPS19 40s ribosomal protein s19. [swissprot;acc:p39019] Subtracted 234.025 224.958 9.067
    821 HDLBP vigilin (high density lipoprotein-binding protein) (hdl-binding protein). [swissprot;acc:q00341] Low confidence 201.169 196.014 5.155
    IMP4 u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Divided High confidence 221.676 231.453 1.0441
    PEX5 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Low confidence 208.488 203.181 1.02612
    RPL31 60s ribosomal protein l31. [swissprot;acc:p12947] Subtracted High confidence 234.025 224.958 9.067
    822 ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Divided Low confidence 208.488 203.181 1.02612
    EIF3B eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] High confidence 243.067 232.805 1.04408
    MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Subtracted 55 46 9
    UPF1 regulator of nonsense transcripts 1 (nonsense mrna reducing factor 1) (norf1) (up-frameshift suppressor 1 homolog). [swissprot;acc:q92900] Low confidence 202.069 196.914 5.155
    823 C16orf80 transcription factor iib. [refseq;acc:nm_013242] Divided High confidence 206.068 197.471 1.04354
    EIF3D eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Subtracted Low confidence 205.551 200.398 5.153
    MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence 55 46 9
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Divided Low confidence 186.275 181.537 1.0261
    824 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted High confidence 55 46 9
    PNKD myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Low confidence 200.782 195.631 5.151
    SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Divided High confidence 206.068 197.471 1.04354
    ZNF423 olf-1/ebf associated zinc finger protein; smad- and olf-interacting zinc finger protein. [refseq;acc:nm_015069] Low confidence 204.922 199.711 1.02609
    825 no value 40s ribosomal protein s3a. [swissprot;acc:p49241] Subtracted High confidence 225.689 234.674 8.985
    early hematopoietic zinc finger. [refseq;acc:nm_015461] Divided Low confidence 204.914 199.706 1.02608
    LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Subtracted 202.15 197.002 5.148
    WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Divided High confidence 206.214 197.614 1.04352
    826 CTSB cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Low confidence 201.026 195.916 1.02608
    DDX39 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Subtracted 192.552 187.412 5.14
    HTATIP 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] Divided High confidence 223.186 213.912 1.04335
    POLR2J dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Subtracted 230.811 239.785 8.974
    827 CCDC22 jm1 protein. [refseq;acc:nm_014008] 219.762 210.806 8.956
    LOH12CR1 loh1cr12. [refseq;acc:nm_058169] Divided 230.087 220.579 1.0431
    MLH3 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Subtracted Low confidence 203.643 198.505 5.138

    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/