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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3180 to 3229 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    398 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked High confidence 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
    PPP6C serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Squared Low confidence 50510.9 47246.5 1.06909
    XAB2 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Measured High confidence 5084.26 5904.1 1.16125
    YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Ranked Low confidence 205.997 213.496 1.0364
    399 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Squared High confidence 18929.1 23222.8 1.22683
    ATP5G2 atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p2) (atpase protein 9) (atpase subunit c). [swissprot;acc:q06055] Low confidence 52285.1 48907.2 1.06907
    CCNG2 cyclin g2. [swissprot;acc:q16589] Rooted High confidence 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
    FMO4 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Measured Low confidence 7680.62 8085.57 1.05272
    GTF3A transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Ranked 193.291 186.506 1.03638
    HAAO 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Rooted 84.6421 88.7007 1.04795
    400 ADCY6 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Measured High confidence 5201.41 4479.76 1.16109
    CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] Rooted 116.707 106.044 1.10055
    DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Squared Low confidence 45694.9 42750.3 1.06888
    GYS1 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] High confidence 39478.8 48419 1.22646
    MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Measured Low confidence 6970.25 7337.73 1.05272
    PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] Ranked High confidence 207.908 226.218 1.08807
    SLC35E1 solute carrier family 35, member e1. [refseq;acc:nm_024881] Low confidence 203.661 211.03 1.03618
    TP63 tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Rooted 75.7411 79.3726 1.04795
    401 no value sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Ranked 205.017 197.863 1.03616
    ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured High confidence 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
    GMPPA gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Measured Low confidence 10800.7 10260 1.0527
    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 High confidence 116.707 106.044 1.10055
    PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Squared Low confidence 45694.9 42750.3 1.06888
    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 High confidence 207.908 226.218 1.08807
    TP73 tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Rooted Low confidence 75.7395 79.3703 1.04794
    402 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared High confidence 39472 48393.1 1.22601
    ARIH2 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Low confidence 48608.6 45485.7 1.06866
    EIF6 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted High confidence 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
    SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Measured Low confidence 7934.21 8352.26 1.05269
    TP53 cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Rooted 75.7377 79.3677 1.04793
    TREX2 x-linked protein sts1769. [swissprot;acc:q99871] Ranked 211.253 203.883 1.03615
    403 ATRIP three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166]
    EEF1B2 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Rooted 70.3162 73.6827 1.04788
    FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured High confidence 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
    PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 226.218 1.08807
    PREP prolyl endopeptidase (ec 3.4.21.26) (post-proline cleaving enzyme) (pe). [swissprot;acc:p48147] Squared Low confidence 48608.6 45485.7 1.06866
    SARS2 seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Measured 8853.13 9319.56 1.05269
    404 ADSS adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared High confidence 26819.1 32855.4 1.22507
    ATP5G3 atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p3) (atpase protein 9) (atpase subunit c). [swissprot;acc:p48201] Low confidence 52108.1 48765.3 1.06855
    CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Rooted 72.2476 75.7022 1.04782
    GRM2 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Ranked 203.081 196 1.03613
    KIF23 kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Measured 10008.8 9508.16 1.05265

    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/