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 Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3101 to 3150 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    776 no value dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Ranked 225.996 215.535 1.04854
    sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Rooted 59.6869 63.6262 1.066
    GDAP1L1 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Measured 5874.76 6533.36 1.11211
    RPS13 40s ribosomal protein s13. [swissprot;acc:q02546] Squared 21976 25607.9 1.16527
    777 DDX39 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Measured 5874.74 6533.34 1.11211
    HDAC1 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Ranked 225.989 215.53 1.04853
    KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Squared 33908.1 39510.9 1.16523
    SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Rooted 59.6869 63.6262 1.066
    778 ATP6V1B1 vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Measured 5874.63 6533.23 1.11211
    MAD2L1 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] Squared 32174 37487.2 1.16514
    SNX6 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Ranked 209.191 219.332 1.04848
    SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Rooted 59.6869 63.6262 1.066
    779 ATP13A2 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Squared 32174 37487.2 1.16514
    DCTD deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Ranked 230.516 241.641 1.04826
    GDAP1 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Measured 5874.76 6533.36 1.11211
    SPRY2 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Rooted 59.6869 63.6262 1.066
    780 ATP6V1D vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Measured 5874.76 6533.36 1.11211
    PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] Rooted 62.2361 58.3858 1.06595
    POLR2F dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Ranked 232.762 243.933 1.04799
    TBP tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Squared 32174 37487.2 1.16514
    781 MRTO4 ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Ranked 245.84 257.636 1.04798
    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] Rooted 62.2361 58.3858 1.06595
    SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490] Measured 5874.76 6533.36 1.11211
    TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Squared 33900.6 39498 1.16511
    782 no value translin. [swissprot;acc:q15631] Ranked 224.385 235.131 1.04789
    ATP6V1H vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Measured 5874.74 6533.33 1.11211
    KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Squared 33893.6 39486.1 1.165
    RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Rooted 62.2361 58.3858 1.06595
    783 no value hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Squared 27407.7 31927.7 1.16492
    ATP6V1B2 vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Measured 5874.78 6533.37 1.1121
    PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Rooted 62.2361 58.3858 1.06595
    TSNAX translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Ranked 224.385 235.131 1.04789
    784 no value dc11 protein. [refseq;acc:nm_020186] Squared 27407.7 31927.7 1.16492
    ATP6V1E1 vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Measured 5874.77 6533.36 1.1121
    PQBP1 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Ranked 224.385 235.131 1.04789
    RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] Rooted 62.2361 58.3858 1.06595
    785 APPBP1 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Squared 27407.7 31927.7 1.16492
    CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Rooted 62.2332 58.3925 1.06577
    HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Measured 4997 5557.17 1.1121
    NET1 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Ranked 244.447 233.508 1.04685
    786 ALAS2 5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] Squared 27407.7 31927.7 1.16492
    ARHGEF3 rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Ranked 244.447 233.508 1.04685
    PC pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Measured 9304.83 10347.3 1.11204
    RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] Rooted 52.0101 48.813 1.0655
    787 no value uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 64.5489 68.7769
    ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Measured 5890.49 6547.9 1.11161
    UBE1C ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Squared 27407.7 31927.7 1.16492
    UTP20 down-regulated in metastasis. [refseq;acc:nm_014503] Ranked 244.447 233.508 1.04685
    788 no value ero1-like. [refseq;acc:nm_014584] Rooted 64.5489 68.7769 1.0655
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Ranked 138.705 132.538 1.04653

    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/