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 Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 958 to 1007 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 1050 HSD17B1 211.449 217.998 1.03097
    estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] 1768 HSD17B4 185.276 187.534 1.01219
    estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 1042 no value 186.799 181.127 1.03132
    ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] 2378 ETNK1 212.724 213.574 1.004
    ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] 2377 ETNK2
    ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 1758 PCYT2 233.45 230.595 1.01238
    eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765] 2868 SNORA67 0.00001 0.00001 1
    eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [swissprot;acc:q14240] 2888 EIF4A2
    eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] 772 ETF1 210.946 221.225 1.04873
    eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] 1341 EIF2S1 226.433 231.491 1.02234
    eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] 1839 EIF2S2 221.525 224.001 1.01118
    eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 1865 EIF2S3 221.639 224.046 1.01086
    eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] 904 EIF3A 246.354 237.223 1.03849
    eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] 1565 EIF3K 221.128 224.767 1.01646
    eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 746 EIF3I 250.465 238.38 1.0507
    eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 903 EIF3G 246.354 237.223 1.03849
    eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] 1571 EIF3EIP 221.128 224.767 1.01646
    eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] 1931 EIF3D 219.753 217.574 1.01001
    eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 1405 EIF3C 245.532 240.483 1.021
    eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 822 EIF3B 243.067 232.805 1.04408
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 252 EIF4G1 237.292 212.457 1.11689
    eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 246 EIF4G3 237.312 212.363 1.11748
    eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 649 EIF4E 233.725 220.751 1.05877
    eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 268 EIF5 271.016 244.167 1.10996
    eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] 2102 EIF5AP1 208.727 210.263 1.00736
    eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 545 EIF6 248.866 233.287 1.06678
    evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] 573 GPATCH1 227.86 213.945 1.06504
    evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] 2092 ECSIT 211.992 210.369 1.00772
    exocyst complex component exo70. [swissprot;acc:q9upt5] 2781 EXOC7 0.00001 0.00001 1
    exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] 721 EXOC5 214.765 203.8 1.0538
    exocyst complex component sec15a. [swissprot;acc:q8tag9] 750 EXOC6 222.138 211.503 1.05028
    exocyst complex component sec15b. [swissprot;acc:q9y2d4] 749 EXOC6B 221.968 211.326 1.05036
    exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] 2487 EXOC1 218.093 218.72 1.00287
    exocyst complex component sec5. [swissprot;acc:q96kp1] 986 EXOC2 116.771 120.707 1.03371
    exocyst complex component sec6. [swissprot;acc:o60645] 981 EXOC3 207.186 200.398 1.03387
    exocyst complex component sec8. [swissprot;acc:q96a65] 869 EXOC4 217.762 209.449 1.03969
    exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] 1344 EXO1 216.772 221.594 1.02224
    exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] 523 EXOSC2 215.237 230.07 1.06891
    exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] 524 EXOSC3
    exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 521 EXOSC4
    exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] 525 EXOSC5
    exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] 1497 XPO1 224.476 220.363 1.01866
    eyes absent homolog 1. [swissprot;acc:q99502] 1396 EYA1 218.463 213.872 1.02147
    eyes absent homolog 2. [swissprot;acc:o00167] 1399 EYA2 218.417 213.848 1.02137
    eyes absent homolog 3. [swissprot;acc:q99504] 1376 EYA3 218.537 213.91 1.02163
    eyes absent homolog 4. [swissprot;acc:o95677] 1398 EYA4 218.449 213.864 1.02144
    ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423] 3228 SCYL3 0.00001 0.00001 1
    f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 1824 CAPZA1 214.722 212.281 1.0115
    f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 1831 no value 214.746 212.328 1.01139
    f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] 2032 CAPZA3 215.322 213.46 1.00872

    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/