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 [...,...].
    Hugo description Rank Gene Value Type Network Comparison Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 51 to 100 of 3228 in total
    Hugo  : no value
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		red
    		green
    		network_comparison
    atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 149 142 170 1.19718
    atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 2727 221.001 220.927 1.00033
    ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 2148 217.871 219.366 1.00686
    ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 452 224.161 207.972 1.07784
    ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 1568 221.128 224.767 1.01646
    basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 2715 216.018 215.903 1.00053
    beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 2221 221.509 220.108 1.00637
    bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 271 241.373 267.352 1.10763
    block 23. [sptrembl;acc:q8nhw5] 1091 226.205 232.858 1.02941
    blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 1930 196.964 198.935 1.01001
    1932 196.965 198.936
    bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 1748 215.673 212.971 1.01269
    brain protein 16. [refseq;acc:nm_016458] 1847 216.811 219.195 1.011
    c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 321 241.892 265.959 1.09949
    calmodulin. [swissprot;acc:p02593] 2928 0.00001 0.00001 1
    casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 1710 227.225 224.21 1.01345
    casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] 936 232.473 224.372 1.03611
    cbf1 interacting corepressor. [refseq;acc:nm_004882] 572 227.86 213.945 1.06504
    ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 3226 0.00001 0.00001 1
    cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 832 231.734 222.222 1.0428
    collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 1990 219.26 217.194 1.00951
    creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 1938 198.293 196.341 1.00994
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1452 160.381 163.554 1.01978
    cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 1423 221.152 216.659 1.02074
    cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 1170 219.399 213.784 1.02626
    cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 797 224.244 234.511 1.04578
    dc11 protein. [refseq;acc:nm_020186] 2489 194.527 195.08 1.00284
    dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 1385 218.47 213.875 1.02148
    dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 634 226.523 213.786 1.05958
    dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 1591 225.119 228.769 1.01621
    dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 1009 229.116 221.823 1.03288
    disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 708 220.438 209.118 1.05413
    dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 724 244.842 232.577 1.05274
    dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 776 225.996 215.535 1.04854
    dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 576 235.18 250.419 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
    dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 700 220.438 209.118 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
    dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1881 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
    dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 339 243.583 267.527 1.0983
    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] 906 230.764 239.62 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
    dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 1790 203.759 201.349 1.01197
    dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 1071 231.277 238.356 1.03061
    dok-like protein. [refseq;acc:nm_024872] 653 216.504 204.622 1.05807
    dpy-30-like protein. [swissprot;acc:q9c005] 1815 220.462 217.926 1.01164
    dystrophin. [swissprot;acc:p11532] 2584 213.422 213.75 1.00154
    elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 1791 217.866 215.295 1.01194

    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/