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 description Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1425 to 1474 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1425 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] CTSL2 214.717 219.157 1.02068
    1426 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] CTSL1
    1427 sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] ATP1A3
    1428 sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] ATP1A2
    1429 wd repeat domain 26. [refseq;acc:nm_025160] WDR26 213.351 217.74 1.02057
    1430 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] DUT 187.114 190.925 1.02037
    1431 uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] RAD23A 220.987 225.468 1.02028
    1432 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036] PSMD4
    1433 inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] OCRL
    1434 uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] RAD23B
    1435 myosin vi. [swissprot;acc:q9um54] no value
    1436 similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] EVI5L 218.829 214.493 1.02022
    1437 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] EVI5
    1438 geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] PGGT1B 225.039 229.573 1.02015
    1439 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] FADS3
    1440 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] SMAD4
    1441 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] FADS2
    1442 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] no value
    1443 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] GLUD2 203.908 207.998 1.02006
    1444 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] GLUDP5
    1445 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] PCF11 134.233 136.922 1.02003
    1446 heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] HSPB1 221.817 226.23 1.01989
    1447 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] POLE3 250.854 255.842 1.01988
    1448 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] ZMPSTE24 226.532 222.117
    1449 transportin-sr; importin 12. [refseq;acc:nm_012470] TNPO3 225.305 229.766 1.0198
    1450 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] HSPB8 221.804 226.194 1.01979
    1451 my016 protein. [sptrembl;acc:q9h3k6] BOLA2B 224.755 229.2 1.01978
    1452 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] no value 160.381 163.554
    1453 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] RTN4 207.038 211.13 1.01976
    1454 sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] SAP18 207.024 211.089 1.01964
    1455 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] EHD1 211.085 1.01962
    1456 eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] EHD4 211.086
    1457 eh-domain containing protein 2. [swissprot;acc:q9nzn4] EHD2
    1458 eh-domain containing protein 3. [swissprot;acc:q9nzn3] EHD3
    1459 importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] CSE1L 192.336 188.637 1.01961
    1460 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] TRIP12 205.817 209.851 1.0196
    1461 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] RTN1 207.019 211.077
    1462 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] DLSTP 205.817 209.851
    1463 pnas-18. [sptrembl;acc:q9bzu3] no value 161.056 164.211 1.01959
    1464 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 217.351 213.18 1.01957
    1465 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] MTO1
    1466 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] RTN2 207.022 211.073
    1467 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] MPP2 228.513 232.983 1.01956
    1468 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] DRAP1 212.001 207.937 1.01954
    1469 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] RTN3 207.013 211.05 1.0195
    1470 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] QARS 221.412 217.199 1.0194
    1471 spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] SRM
    1472 glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] GARS
    1473 glutamyl trna synthetase. [sptrembl;acc:o14563] EARS2
    1474 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] RANBP5 218.582 214.427 1.01938

    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/