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 Filtered Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 1451 to 1500 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Interaction Map  : High confidence
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    1451 BOLA2B my016 protein. [sptrembl;acc:q9h3k6] 224.755 229.2 1.01978
    1452 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 160.381 163.554
    1453 RTN4 reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] 207.038 211.13 1.01976
    1454 SAP18 sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] 207.024 211.089 1.01964
    1455 EHD1 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 211.085 1.01962
    1456 EHD4 eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] 211.086
    1457 EHD2 eh-domain containing protein 2. [swissprot;acc:q9nzn4]
    1458 EHD3 eh-domain containing protein 3. [swissprot;acc:q9nzn3]
    1459 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 192.336 188.637 1.01961
    1460 TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 205.817 209.851 1.0196
    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] 161.056 164.211 1.01959
    1464 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 217.351 213.18 1.01957
    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] 228.513 232.983 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
    1469 RTN3 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 207.013 211.05 1.0195
    1470 QARS glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 221.412 217.199 1.0194
    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] 218.582 214.427 1.01938
    1475 KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 181.882 178.438 1.0193
    1476 RANBP6 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 218.591 214.457 1.01928
    1477 no value transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] 215.328 211.267 1.01922
    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] 228.469 232.855 1.0192
    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] 218.664 214.55 1.01918
    1481 CDC23 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 208.432 204.516 1.01915
    1482 LSAMP limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 224.354 220.15 1.0191
    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] 207.877 203.989 1.01906
    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] 213.251 209.264 1.01905
    1490 PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] 221.961 226.186 1.01903
    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] 217.704 221.839 1.01899
    1492 OPCML opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 224.159 220.017 1.01883
    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] 204.146 207.988 1.01882
    1494 PDHA1 pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] 204.133 207.967 1.01878
    1495 CSNK1A1L casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 225.237 1.01874
    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] 224.476 220.363 1.01866
    1498 no value neurotrimin precursor (hnt). [swissprot;acc:q9p121] 224.022 219.924 1.01863
    1499 DCP1A transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 224.509 220.411 1.01859
    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] 213.398 209.52 1.01851

    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/