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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2908 to 2957 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    1454 SAP18 sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Divided 207.024 211.089 1.01964
    1455 EHD1 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 211.085 1.01962
    EHD2 eh-domain containing protein 2. [swissprot;acc:q9nzn4] Subtracted 211.086 4.062
    1456 EHD3 eh-domain containing protein 3. [swissprot;acc:q9nzn3]
    EHD4 eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] Divided 1.01962
    1457 no value transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Subtracted 215.328 211.267 4.061
    EHD2 eh-domain containing protein 2. [swissprot;acc:q9nzn4] Divided 207.024 211.086 1.01962
    1458 EHD1 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] Subtracted 211.085 4.061
    EHD3 eh-domain containing protein 3. [swissprot;acc:q9nzn3] Divided 211.086 1.01962
    1459 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 192.336 188.637 1.01961
    RTN1 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Subtracted 207.019 211.077 4.058
    1460 SFRS10 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 215.122 211.066 4.056
    TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Divided 205.817 209.851 1.0196
    1461 MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Subtracted 171.231 167.177 4.054
    RTN1 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Divided 207.019 211.077 1.0196
    1462 DLSTP dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] 205.817 209.851
    SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Subtracted 171.231 167.177 4.054
    1463 no value pnas-18. [sptrembl;acc:q9bzu3] Divided 161.056 164.211 1.01959
    DPAGT1 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Subtracted 171.231 167.177 4.054
    1464 no value poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Divided 217.351 213.18 1.01957
    DLC1 rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Subtracted 171.231 167.177 4.054
    1465 MAPKAPK2 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
    MTO1 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Divided 217.351 213.18 1.01957
    1466 CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Subtracted 171.231 167.177 4.054
    RTN2 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Divided 207.022 211.073 1.01957
    1467 ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] Subtracted 171.231 167.177 4.054
    MPP2 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Divided 228.513 232.983 1.01956
    1468 DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] 212.001 207.937 1.01954
    STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Subtracted 171.231 167.177 4.054
    1469 RTN3 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Divided 207.013 211.05 1.0195
    STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Subtracted 171.231 167.177 4.054
    1470 CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
    QARS glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Divided 221.412 217.199 1.0194
    1471 MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Subtracted 171.231 167.177 4.054
    SRM spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Divided 221.412 217.199 1.0194
    1472 GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
    MAPK14 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Subtracted 171.231 167.177 4.054
    1473 CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]
    EARS2 glutamyl trna synthetase. [sptrembl;acc:o14563] Divided 221.412 217.199 1.0194
    1474 CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Subtracted 171.231 167.177 4.054
    RANBP5 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Divided 218.582 214.427 1.01938
    1475 KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 181.882 178.438 1.0193
    SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Subtracted 171.231 167.177 4.054
    1476 RANBP6 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Divided 218.591 214.457 1.01928
    RTN2 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Subtracted 207.022 211.073 4.051
    1477 no value transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Divided 215.328 211.267 1.01922
    RTN3 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Subtracted 207.013 211.05 4.037
    1478 SFRS10 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Divided 215.122 211.066 1.01922
    TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Subtracted 205.817 209.851 4.034
    1479 DLSTP dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]

    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/