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 2575 to 2624 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    Hugo
    description
    Value Type
    red
    green
    network_comparison
    644 PFKP 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Squared 16156.3 19046 1.17886
    POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] Rooted 51.1896 47.4617 1.07855
    645 no value nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Squared 22722.5 26786.5 1.17885
    GSTT1 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Measured 4810.71 5413.89 1.12538
    HTATSF1 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Ranked 217.67 230.596 1.05938
    MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Rooted 63.1463 68.1044 1.07852
    646 no value 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Squared 27898 32866.2 1.17808
    DNAJB11 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Rooted 63.1463 68.1044 1.07852
    FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Measured 4019.88 4522.61 1.12506
    SCOC short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Ranked 216.731 229.549 1.05914
    647 CAPNS1 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Rooted 64.5657 69.6237 1.07834
    CTSB cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Squared 33384.2 39324.9 1.17795
    DYNLL2 dynein light chain 2. [refseq;acc:nm_080677] Ranked 216.731 229.549 1.05914
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Measured 5167.88 4594.43 1.12481
    648 ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Rooted 64.5685 69.6269 1.07834
    MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Ranked 218.227 206.078 1.05895
    RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Squared 29174 34363.5 1.17788
    SF3A3 splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Measured 5248.07 5901.72 1.12455
    649 EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Ranked 233.725 220.751 1.05877
    GCA grancalcin. [swissprot;acc:p28676] Rooted 64.5659 69.624 1.07834
    RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Squared 29173.8 34362.7 1.17786
    SF3A1 splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Measured 5248.07 5901.72 1.12455
    650 no value u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Ranked 228.986 216.276 1.05877
    CDYL2 chromodomain y-like protein 2. [refseq;acc:nm_152342] Squared 29016.1 34169.2 1.17759
    GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Measured 8362.81 9402.7 1.12435
    SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Rooted 64.566 69.6241 1.07834
    651 BAIAP3 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Ranked 233.725 220.751 1.05877
    CDY1B testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Squared 29012.2 34163.9 1.17757
    PDCD6 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Rooted 64.5685 69.6269 1.07834
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Measured 5168.43 4597.44 1.1242
    652 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Ranked 248.994 235.255 1.0584
    ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Rooted 64.5672 69.6254 1.07834
    CDYL chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] Squared 29012.2 34163.9 1.17757
    TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Measured 5168.43 4597.44 1.1242
    653 no value dok-like protein. [refseq;acc:nm_024872] Ranked 216.504 204.622 1.05807
    CDY2B testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Squared 29012.4 34164 1.17757
    MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Measured 5560.06 6248.27 1.12378
    SORBS2 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Rooted 64.4927 69.539 1.07825
    654 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Measured 4088.63 4593.43 1.12346
    sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Squared 27174.1 31992.4 1.17731
    CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Rooted 59.9021 64.5838 1.07816
    DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Ranked 216.504 204.622 1.05807
    655 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Measured 4088.63 4593.43 1.12346
    DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Ranked 216.504 204.622 1.05807
    HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Rooted 59.9021 64.5838 1.07816
    SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Squared 27174.1 31992.4 1.17731
    656 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Measured 6139.04 6893.7 1.12293
    FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Ranked 216.504 204.622 1.05807
    SIM1 single-minded homolog 1. [swissprot;acc:p81133] Rooted 59.9021 64.5838 1.07816
    SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Squared 27174.1 31992.4 1.17731

    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/