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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2451 to 2500 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Value Type
    		description
    		red
    		green
    		network_comparison
    613 Squared n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 17550.2 20701.1 1.17954
    Rooted n-myc proto-oncogene protein. [swissprot;acc:p04198] 57.1971 61.7626 1.07982
    614 Measured solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] 11222.2 9948.93 1.12798
    Ranked homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 214.257 202.125 1.06002
    Squared coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 51527.6 43689.1 1.17942
    Rooted ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 57.2007 61.7615 1.07973
    615 Measured cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 11222.2 9948.93 1.12798
    Ranked homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 214.257 202.132 1.05999
    Squared coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] 51527.6 43689.1 1.17942
    Rooted ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] 57.2007 61.7615 1.07973
    616 Measured catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 11222.2 9948.93 1.12798
    Ranked homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 214.257 202.132 1.05999
    Squared coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] 51527.6 43689.1 1.17942
    Rooted nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] 57.2007 61.7615 1.07973
    617 Measured dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 5162.52 5822.47 1.12783
    Ranked homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 214.257 202.135 1.05997
    Squared coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] 51527.6 43689.1 1.17942
    Rooted elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 57.2008 61.7614 1.07973
    618 Measured nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 7878.27 8879.08 1.12703
    Ranked gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 214.256 202.139 1.05994
    Squared peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 51527.6 43689.1 1.17942
    Rooted myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 57.208 61.7592 1.07956
    619 Measured nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 3879.99 4371.24 1.12661
    Ranked forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 214.256 202.139 1.05994
    Squared coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] 51527.6 43689.1 1.17942
    Rooted dendritic cell protein. [refseq;acc:nm_006360] 63.847 68.8873 1.07894
    620 Measured ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 6227.87 7012.9 1.12605
    Ranked gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 214.256 202.14 1.05994
    Squared homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 32208.8 37986.6 1.17939
    Rooted potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 63.847 68.8873 1.07894
    621 Measured ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 4115.39 4633.96 1.12601
    Ranked gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 214.256 202.14 1.05994
    Squared nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 32193.3 37967.7 1.17937
    Rooted 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] 63.847 68.8873 1.07894
    622 Measured mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 6228.42 7013.21 1.126
    Ranked gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 214.256 202.14 1.05994
    Squared gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 32192.5 37966.8 1.17937
    Rooted cpz gene product. [refseq;acc:nm_003652] 63.847 68.8873 1.07894
    623 Measured cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 6228.39 7013.19 1.126
    Ranked gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 214.256 202.14 1.05994
    Squared similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 32193.3 37967.7 1.17937
    Rooted carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 63.847 68.8873 1.07894
    624 Measured dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 6228.39 7013.19 1.126
    Ranked interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 214.256 202.139 1.05994
    Squared forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 32192.5 37966.8 1.17937
    Rooted potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 63.847 68.8873 1.07894
    625 Measured 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] 6228.39 7013.19 1.126
    Ranked gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 214.256 202.14 1.05994
    Squared gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 32192.6 37966.9 1.17937
    Rooted serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] 59.6678 64.3767 1.07892

    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
    - 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/