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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2008 to 2057 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    126 Divided STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked High confidence 94 1.21277 114
    Subtracted AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Squared 71387.4 24646 96033.4
    FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Ranked 285.684 33.45 252.234
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 14.1587 75.094
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured Low confidence 7098.44 786.54 7884.98
    NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Ranked 226.892 13.231 213.661
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Rooted 67.0736 5.3742 72.4478
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 58331.7 7295.7 51036
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Measured High confidence 450.5 1944 2394.5
    127 Divided no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared 88432.6 1.51365 58423.3
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured Low confidence 11285.3 1.0937 10318.5
    CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked High confidence 94 1.21277 114
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 1.23236 75.094
    JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 1.33436 7523.39
    SLC16A2 monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] Squared Low confidence 63904 1.13908 72791.6
    VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Ranked 203.678 1.06705 190.88
    VPS41 vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Rooted 70.0842 1.07532 75.3627
    Subtracted APC adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] Ranked 222.31 13.228 235.538
    CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared 58384.8 7288.1 51096.7
    CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Ranked High confidence 285.684 33.45 252.234
    DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 13.58 166.771
    MAN1B1 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Low confidence 66.9562 5.3681 72.3243
    MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared High confidence 71386.9 24645.6 96032.5
    PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Measured Low confidence 10087.8 783.1 10870.9
    RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 450.5 1944 2394.5
    128 Divided no value pnas-18. [sptrembl;acc:q9bzu3] Squared 87787.3 1.50952 58155.8
    LENG4 malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Rooted Low confidence 64.4748 1.0739 60.0381
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured High confidence 4355.61 1.3341 5810.82
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Low confidence 11285.3 1.0937 10318.5
    SLC16A10 solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] Squared 63903.1 1.13907 72790.2
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Ranked High confidence 94 1.21277 114
    STRN striatin. [swissprot;acc:o43815] Low confidence 214.085 1.06618 200.796
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted High confidence 48.0515 1.23069 39.0445
    Subtracted APC2 adenomatous polyposis coli like. [refseq;acc:nm_005883] Ranked Low confidence 222.34 13.207 235.547
    AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Squared High confidence 71346.6 24618.5 95965.1
    PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Low confidence 60522.9 7198.1 67721
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked High confidence 285.684 33.45 252.234
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted Low confidence 66.9562 5.3681 72.3243
    PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Measured 7263.76 782.53 8046.29
    TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] High confidence 11004.2 1940 12944.2
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 13.3216 67.9743
    129 Divided COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Ranked Low confidence 220.969 1.06609 235.572
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured High confidence 4358.13 1.33348 5811.49
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Low confidence 11285.3 1.0937 10318.5
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted High confidence 54.2343 1.23044 66.7323
    NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Low confidence 62.9048 1.07372 67.5424
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared High confidence 178263 1.50257 118639
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 56860.4 1.13764 64686.5
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked High confidence 94 1.21277 114
    Subtracted CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] 285.684 33.45 252.234

    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/