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 green network_comparison
    Results: HTML CSV LaTeX Showing element 733 to 782 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    733 ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 164 155.961 1.05154
    734 no value presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 232.601 244.534 1.0513
    735 RANP1 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
    736 no value presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
    737 SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] 125.526 119.402 1.05129
    738 XAB2 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 222.825 211.966 1.05123
    739 PFAS phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] 223.58 235.027 1.0512
    740 ATIC 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]
    741 PAICS 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]
    742 BRP44 brain protein 44. [swissprot;acc:o95563] 126.215 120.078 1.05111
    743 SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]
    744 SEPT6 septin 6. [swissprot;acc:q14141] 126.604 120.463 1.05098
    745 SLC35B1 solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] 214.679 225.568 1.05072
    746 EIF3I eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 250.465 238.38 1.0507
    747 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575]
    748 FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 245.246 233.483 1.05038
    749 EXOC6B exocyst complex component sec15b. [swissprot;acc:q9y2d4] 221.968 211.326 1.05036
    750 EXOC6 exocyst complex component sec15a. [swissprot;acc:q8tag9] 222.138 211.503 1.05028
    751 no value u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 223.463 212.875 1.04974
    752 SLU7 step ii splicing factor slu7. [refseq;acc:nm_006425]
    753 LBP lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 224.434 235.583 1.04968
    754 SPCS2 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
    755 UMPS 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]
    756 CLPTM1 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
    757 BPI bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]
    758 PLTP phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]
    759 OSTF1 osteoclast stimulating factor 1. [swissprot;acc:q92882] 231.809 243.289 1.04952
    760 NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] 246.055 234.458 1.04946
    761 CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 213.325 203.303 1.0493
    762 CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 213.256 203.237
    763 N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 228.78 218.091 1.04901
    764 PRPF3 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 222.082 211.707
    765 HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 229.045 218.343
    766 TRIOBP protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 213.804 224.226 1.04875
    767 no value rho interacting protein 3. [refseq;acc:nm_015134] 213.803 224.224 1.04874
    768 DNAJB4 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 210.946 221.225 1.04873
    769 PERLD1 cab2. [refseq;acc:nm_033419]
    770 DNAJB5 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]
    771 DNAJB1 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685]
    772 ETF1 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]
    773 VPS52 suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]
    774 MCFD2 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 1.04854
    775 no value histone deacetylase 2 (hd2). [swissprot;acc:q92769] 226.003 215.541
    776 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 225.996 215.535
    777 HDAC1 histone deacetylase 1 (hd1). [swissprot;acc:q13547] 225.989 215.53 1.04853
    778 SNX6 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] 209.191 219.332 1.04848
    779 DCTD deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] 230.516 241.641 1.04826
    780 POLR2F dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] 232.762 243.933 1.04799
    781 MRTO4 ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] 245.84 257.636 1.04798
    782 no value translin. [swissprot;acc:q15631] 224.385 235.131 1.04789

    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/