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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1458 to 1507 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		network_comparison
    		green
    1458 EHD3 eh-domain containing protein 3. [swissprot;acc:q9nzn3] 207.024 1.01962 211.086
    1459 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 192.336 1.01961 188.637
    1460 TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 205.817 1.0196 209.851
    1461 RTN1 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] 207.019 211.077
    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
    1463 no value pnas-18. [sptrembl;acc:q9bzu3] 161.056 1.01959 164.211
    1464 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 217.351 1.01957 213.18
    1465 MTO1 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]
    1466 RTN2 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] 207.022 211.073
    1467 MPP2 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 228.513 1.01956 232.983
    1468 DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] 212.001 1.01954 207.937
    1469 RTN3 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 207.013 1.0195 211.05
    1470 QARS glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 221.412 1.0194 217.199
    1471 SRM spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]
    1472 GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
    1473 EARS2 glutamyl trna synthetase. [sptrembl;acc:o14563]
    1474 RANBP5 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] 218.582 1.01938 214.427
    1475 KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 181.882 1.0193 178.438
    1476 RANBP6 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 218.591 1.01928 214.457
    1477 no value transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] 215.328 1.01922 211.267
    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] 215.122 211.066
    1479 MPP6 maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] 228.469 1.0192 232.855
    1480 CPSF6 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] 218.664 1.01918 214.55
    1481 CDC23 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 208.432 1.01915 204.516
    1482 LSAMP limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 224.354 1.0191 220.15
    1483 PDHB pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] 198.927 202.726
    1484 TMEM91 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]
    1485 RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 207.877 1.01906 203.989
    1486 HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
    1487 HIVEP1 zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]
    1488 HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
    1489 MAP3K7 mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] 213.251 1.01905 209.264
    1490 PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] 221.961 1.01903 226.186
    1491 GPI glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] 217.704 1.01899 221.839
    1492 OPCML opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 224.159 1.01883 220.017
    1493 PDHA2 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] 204.146 1.01882 207.988
    1494 PDHA1 pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] 204.133 1.01878 207.967
    1495 CSNK1A1L casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 1.01874 225.237
    1496 CSNK1A1 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729]
    1497 XPO1 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] 224.476 1.01866 220.363
    1498 no value neurotrimin precursor (hnt). [swissprot;acc:q9p121] 224.022 1.01863 219.924
    1499 DCP1A transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 224.509 1.01859 220.411
    1500 COPS4 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 213.398 1.01851 209.52
    1501 KIFC3 kinesin family member c3. [refseq;acc:nm_005550] 214.727 1.01845 210.838
    1502 no value uridine kinase-like 1. [swissprot;acc:q9nwz5] 218.084 1.01838 214.149
    1503 KRR1 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 242.181 1.01828 237.834
    1504 CDC25C m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] 259.439 1.01822 254.797
    1505 CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] 216.158 1.0181 212.316
    1506 C16orf42 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 212.103 1.01807 208.339
    1507 PDK1 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 213.274 1.01801 209.5

    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/