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 Rank Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1758 to 1807 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    myosin heavy chain, smooth muscle isoform (smmhc). [swissprot;acc:p35749] 2985 MYH11 0.00001 0.00001 1
    myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] 1764 no value 233.45 230.595 1.01238
    myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] 1760 MYL1
    myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] 1763 MYL6
    myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] 1761 MYL3
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 152 no value 55 46 1.19565
    myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 150 MYO5B
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 151 MYO5C
    myosin vi. [swissprot;acc:q9um54] 1435 no value 220.987 225.468 1.02028
    myosin viia. [swissprot;acc:q13402] 2639 MYO7A 220.658 220.386 1.00123
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 21 MYO15A 185.678 245.247 1.32082
    myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613] 3190 MTMR1 0.00001 0.00001 1
    myotubularin-related protein 2 (ec 3.1.3.-). [swissprot;acc:q13614] 3166 MTMR2
    n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 1336 GALK2 215.162 210.412 1.02257
    n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70] 3022 NAGK 0.00001 0.00001 1
    n-acetylglutamate synthase. [refseq;acc:nm_153006] 1616 NAGS 223.179 226.611 1.01538
    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] 728 B3GNT1 208.874 219.708 1.05187
    n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] 2394 NAT5 221.662 220.826 1.00379
    n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] 1354 NDST3 228.409 223.475 1.02208
    n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] 1355 NDST4
    n-myc proto-oncogene protein. [swissprot;acc:p04198] 882 MYCN 227.601 219.008 1.03924
    n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 438 ARD1A 233.723 216.674 1.07869
    nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] 1863 CYB5R3 210.856 213.147 1.01087
    nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] 1762 NDUFS6 233.45 230.595 1.01238
    nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 3005 NDUFA5 0.00001 0.00001 1
    nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 119 NDUFS4 318.982 259.004 1.23157
    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] 885 NDUFS8 227.596 219.017 1.03917
    nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404] 2795 NDUFV2 0.00001 0.00001 1
    nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [swissprot;acc:o75489] 3081 PTPMT1
    nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795] 2954 NDUFA9
    nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [swissprot;acc:o75306] 2878 NDUFS2
    nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 630 NDUFA6 214.256 202.141 1.05993
    nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 1096 NDUFB9 212.345 206.339 1.02911
    nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] 2386 NDUFB10 213.82 212.983 1.00393
    nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 118 NDUFA12 284.753 228.934 1.24382
    nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 274 POR 241.373 267.352 1.10763
    nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 2228 FDXR 211.81 213.153 1.00634
    nag14 protein. [refseq;acc:nm_022143] 2240 LRRC4 222.959 224.337 1.00618
    nanos (fragment). [sptrembl;acc:q8wy41] 2803 no value 0.00001 0.00001 1
    nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] 2633 NRD1 224.891 225.195 1.00135
    nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 888 no value 212.027 204.05 1.03909
    necdin. [swissprot;acc:q99608] 90 NDN 88.2482 110.265 1.24949
    nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] 2608 no value 215.497 215.799 1.0014
    neighbor of cox4. [swissprot;acc:o43402] 1818 COX4NB 220.462 217.926 1.01164
    nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] 1060 NLK 218.162 211.648 1.03078
    neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] 2740 no value 198.278 198.321 1.00022
    neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 559 WASL 207.309 194.452 1.06612
    neuralized-like. [refseq;acc:nm_004210] 117 NEURL 332.326 266.948 1.24491
    neurocalcin delta. [swissprot;acc:p29554] 1182 NCALD 225.104 230.931 1.02589
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 129 VPS24 94 114 1.21277

    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/