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 Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 7091 to 7140 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    3863 TNFSF5IP1 hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232] 199.625 197.072 1.01295
    3864 PFKFB3 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (6pf-2-k/fru- 2,6-p2ase brain/placenta-type isozyme) (ipfk-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16875] 194.792 197.306 1.01291
    3865 PFKFB1 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6pf-2-k/fru- 2,6-p2ase liver isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:p16118]
    3866 DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
    3867 PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6pf-2-k/fru- 2,6-p2ase heart-type isozyme) (pfk-2/fbpase-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:o60825]
    3868 PFKFB4 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (6pf-2-k/fru- 2,6-p2ase testis-type isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16877]
    3869 IK red protein (rer protein) (ik factor) (cytokine ik). [swissprot;acc:q13123] 202.263 199.686
    3870 MTAP 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 199.433 196.894 1.0129
    3871 POLR2L dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 202.466 199.89 1.01289
    3872 no value kappa b-ras 1. [refseq;acc:nm_020345] 202.645 200.066
    3873 NKIRAS2 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595]
    3874 C14orf122 protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] 200.283 197.741 1.01286
    3875 CDC20 cell division cycle 20; cell division cycle 20, s.cerevisiae homolog. [refseq;acc:nm_001255] 197.394 194.891 1.01284
    3876 PKMYT1 protein kinase myt1 isoform 1. [refseq;acc:nm_004203] 203.246 200.678 1.0128
    3877 GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 202.706 205.299 1.01279
    3878 MAP2K6 dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] 199.949 197.426 1.01278
    3879 RYBP ring1 and yy1 binding protein; ring1 interactor rybp; yy1 and e4tf1 associated factor 1; apoptin-associating protein 1. [refseq;acc:nm_012234] 200.602 198.072 1.01277
    3880 TTC1 tetratricopeptide repeat protein 1 (tpr repeat protein 1). [swissprot;acc:q99614] 203.586 201.019
    3881 COPS7A cop9 complex subunit 7a; cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 7a. [refseq;acc:nm_016319] 201.889 199.344
    3882 YAF2 yy1 associated factor 2. [refseq;acc:nm_005748] 200.602 198.072
    3883 MRTO4 ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] 203.659 201.094 1.01276
    3884 CCDC47 gk001 protein. [refseq;acc:nm_020198] 199.26 196.752 1.01275
    3885 SLC4A1 band 3 anion transport protein (anion exchange protein 1) (ae 1) (cd233 antigen). [swissprot;acc:p02730] 204.576 202
    3886 MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 204.522 201.949 1.01274
    3887 DPH1 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 202.018 199.477
    3888 SLC4A2 anion exchange protein 2 (non-erythroid band 3-like protein) (bnd3l). [swissprot;acc:p04920] 204.559 201.988 1.01273
    3889 COPS7B cop9 constitutive photomorphogenic homolog subunit 7b; likely ortholog of cop9 (constitutive photomorphogenic), subunit 7b (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 7b. [refseq;acc:nm_022730] 201.902 199.364
    3890 no value ubiquinol-cytochrome c reductase complex 7.2 kda protein (ec 1.10.2.2) (cytochrome c1, nonheme 7 kda protein) (complex iii subunit x) (7.2 kda cytochrome c1-associated protein subunit) (hspc119). [swissprot;acc:q9udw1] 206.614 204.018 1.01272
    3891 TAF1B tbp-associated factor 1b; tata box binding protein (tbp)-associated factor, rna polymerase i, b, 63kd; sl1, 63kd subunit. [refseq;acc:nm_005680] 199.996 197.485 1.01271
    3892 ACOX3 acyl-coenzyme a oxidase 3, peroxisomal (ec 1.3.3.6) (pristanoyl-coa oxidase). [swissprot;acc:o15254]
    3893 COX4NB neighbor of cox4. [swissprot;acc:o43402] 200.352 197.839 1.0127
    3894 SIP1 survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] 202.516 199.978 1.01269
    3895 no value serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 199.187 196.692 1.01268
    3896 block 23. [sptrembl;acc:q8nhw5] 202.202 199.673 1.01267
    3897 RPLP0 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388]
    3898 MAP2K3 dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] 200.15 197.647 1.01266
    3899 no value similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 202.201 199.675 1.01265
    3900 ARHGDIA rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565] 206.72 204.137
    3901 NUP214 nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658] 204.481 201.928 1.01264
    3902 RFX4 regulatory factor x4 isoform b; transcription factor nyd-sp10. [refseq;acc:nm_002920] 203.988 201.442
    3903 RFX1 mhc class ii regulatory factor rfx1 (rfx) (enhancer factor c) (ef-c). [swissprot;acc:p22670] 203.982 201.44 1.01262
    3904 RFX3 transcription factor rfx3. [swissprot;acc:p48380] 203.98 1.01261
    3905 PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 200.957 198.456 1.0126
    3906 NDUFV2 nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404] 203.49 200.959 1.01259
    3907 MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 199.53 197.05
    3908 EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 203.756 201.222
    3909 PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 199.123 196.65 1.01258
    3910 PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 199.122 196.649
    3911 DLG5 discs, large homolog 5 (placenta and prostate dlg) (discs large protein p-dlg). [swissprot;acc:q8tdm6] 207.449 204.872
    3912 SS18 ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [swissprot;acc:q15532] 201.842 199.334

    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/