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 [...,...].
    description Gene Rank Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 758 to 807 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 322 DNASE2B 86.7483 78.8995 1.09948
    deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 1430 DUT 187.114 190.925 1.02037
    destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] 2229 DSTN 217.955 219.336 1.00634
    developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295] 2762 DRG1 0.00001 0.00001 1
    developmentally regulated gtp-binding protein 2 (drg 2). [swissprot;acc:p55039] 3092 DRG2
    dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 174 DGCR14 335 286 1.17133
    dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5] 3006 DGCR8 0.00001 0.00001 1
    di-ras2. [refseq;acc:nm_017594] 892 DIRAS2 212.028 204.055 1.03907
    dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 1591 no value 225.119 228.769 1.01621
    dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] 1298 DLAT 206.482 211.404 1.02384
    dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] 1039 DLD 207.719 214.236 1.03137
    dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] 1462 DLSTP 205.817 209.851 1.0196
    dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] 2392 DHODH 214.966 215.799 1.00388
    dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 1009 no value 229.116 221.823 1.03288
    dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] 2213 DHDH 210.127 211.475 1.00642
    dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] 2288 FMO1 216.607 215.458 1.00533
    dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] 2286 FMO2 216.608 215.456 1.00535
    dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 2276 FMO3 216.613 215.448 1.00541
    dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] 2289 FMO4 216.605 215.46 1.00531
    dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] 2271 FMO5 216.622 215.436 1.00551
    dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 1516 DPP6 213.267 209.511 1.01793
    dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 395 DPP8 218.827 238.407 1.08948
    dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 1515 DPP10 213.267 209.511 1.01793
    dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 394 DPP9 218.827 238.407 1.08948
    diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] 868 MVD 233.298 242.571 1.03975
    diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 1202 DPH2 227.274 233.041 1.02537
    disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] 701 DLGAP1 220.438 209.118 1.05413
    disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 708 no value
    disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] 706 DLGAP3
    disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 710 DLGAP4
    disrupter of silencing 10. [refseq;acc:nm_020368] 1905 UTP3 191.411 193.39 1.01034
    dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 724 no value 244.842 232.577 1.05274
    dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125] 2060 C20orf118 218.79 216.981 1.00834
    dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 776 no value 225.996 215.535 1.04854
    dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] 1287 CYP4A22 218.368 213.22 1.02414
    dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 576 no value 235.18 250.419 1.0648
    dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 2621 224.891 225.195 1.00135
    dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 2408 194.407 193.706 1.00362
    dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] 3025 HMG1L1 0.00001 0.00001 1
    dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 700 no value 220.438 209.118 1.05413
    dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 1125 204.404 210.022 1.02748
    dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 222 MYH7B 112 126 1.125
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 177 NCBP2L 229.406 196.695 1.1663
    dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1881 no value 210.592 208.355 1.01074
    dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] 1329 218.509 213.648 1.02275
    dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 1326 CSMD1
    dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 339 no value 243.583 267.527 1.0983
    dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 1029 DDB1 222.364 215.535 1.03168
    dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 906 no value 230.764 239.62 1.03838
    dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 905 230.768 239.632 1.03841

    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/