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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 713 to 762 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		network_comparison
    		green
    713 dendritic cell protein. [refseq;acc:nm_006360] EIF3M 223.121 1.05402 211.685
    714 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] CPXM2
    715 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] CPN1
    716 cpz gene product. [refseq;acc:nm_003652] CPZ
    717 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] CPE
    718 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] CPXM1
    719 nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] NOL5A 247.769 1.054 235.074
    720 60s acidic ribosomal protein p2. [swissprot;acc:p05387] RPLP2 231.92 1.05396 244.435
    721 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] EXOC5 214.765 1.0538 203.8
    722 trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] TREH 217.952 1.05341 206.902
    723 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] no value 244.842 1.05274 232.577
    724 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
    725 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] MVK 235.296 1.0526 247.673
    726 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] FTSJ3 244.495 1.05196 232.419
    727 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] NUAK1 208.873 1.05188 219.71
    728 n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] B3GNT1 208.874 1.05187 219.708
    729 huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] no value
    730 mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] TIMM10
    731 fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] FH
    732 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] SEPT8 124.434 1.05169 118.318
    733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL 164 1.05154 155.961
    734 presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] no value 232.601 1.0513 244.534
    735 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] RANP1
    736 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] no value
    737 septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 125.526 1.05129 119.402
    738 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] XAB2 222.825 1.05123 211.966
    739 phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] PFAS 223.58 1.0512 235.027
    740 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] ATIC
    741 multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] PAICS
    742 brain protein 44. [swissprot;acc:o95563] BRP44 126.215 1.05111 120.078
    743 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7
    744 septin 6. [swissprot;acc:q14141] SEPT6 126.604 1.05098 120.463
    745 solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] SLC35B1 214.679 1.05072 225.568
    746 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] EIF3I 250.465 1.0507 238.38
    747 trinucleotide repeat containing 15. [refseq;acc:nm_015575] no value
    748 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] FBL 245.246 1.05038 233.483
    749 exocyst complex component sec15b. [swissprot;acc:q9y2d4] EXOC6B 221.968 1.05036 211.326
    750 exocyst complex component sec15a. [swissprot;acc:q8tag9] EXOC6 222.138 1.05028 211.503
    751 u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] no value 223.463 1.04974 212.875
    752 step ii splicing factor slu7. [refseq;acc:nm_006425] SLU7
    753 lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] LBP 224.434 1.04968 235.583
    754 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] SPCS2
    755 uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] UMPS
    756 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] CLPTM1
    757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] BPI
    758 phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] PLTP
    759 osteoclast stimulating factor 1. [swissprot;acc:q92882] OSTF1 231.809 1.04952 243.289
    760 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] NAT10 246.055 1.04946 234.458
    761 signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB 213.325 1.0493 203.303
    762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL 213.256 203.237

    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/