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 Network Comparison Type Gene Hugo Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2062 to 2111 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    516 GALK2 Measured n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 4910.6 5600.61 1.14051
    LSM8 Ranked u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 228.255 213.422 1.0695
    RHOA Squared transforming protein rhoa (h12). [swissprot;acc:p06749] 19987.6 23960.7 1.19878
    517 no value Measured galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] 4910.6 5600.61 1.14051
    Squared splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 19263.3 23092.3 1.19877
    EIF3I Rooted eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 50.0578 54.5502 1.08974
    MTX2 Ranked metaxin 2. [swissprot;acc:o75431] 219.537 234.793 1.06949
    518 no value Rooted trinucleotide repeat containing 15. [refseq;acc:nm_015575] 50.0578 54.5502 1.08974
    GALE Measured udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] 4910.6 5600.61 1.14051
    GNL3 Ranked nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 250.858 234.563 1.06947
    PROSC Squared proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 11447.3 13719.2 1.19847
    519 DVL3 Ranked segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 218.702 204.582 1.06902
    GYS1 Measured glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 9648.27 10994.9 1.13957
    POLI Squared polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 22387.1 26827.3 1.19834
    SEPT8 Rooted septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 114.309 124.527 1.08939
    520 no value Measured endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 9642.22 10986.4 1.13941
    BCAS2 Rooted breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 61.1902 66.6503 1.08923
    PXN Squared paxillin. [swissprot;acc:p49023] 22387.1 26827.3 1.19834
    SLC35D2 Ranked sqv-7-like protein (fragment). [sptrembl;acc:o95454] 214.754 229.565 1.06897
    521 CDC5L Rooted cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 61.1902 66.6503 1.08923
    CPA5 Squared carboxypeptidase a5. [refseq;acc:nm_080385] 53174 44377.4 1.19822
    EXOSC4 Ranked exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 215.237 230.07 1.06891
    PRPF3 Measured u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 5390.78 6142.07 1.13937
    522 CPB1 Squared carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 53174 44377.4 1.19822
    GYS2 Measured glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 9634.98 10976.2 1.1392
    PLRG1 Ranked pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 222.893 208.523 1.06891
    SEPT10 Rooted septin 10 isoform 1. [refseq;acc:nm_144710] 113.733 123.871 1.08914
    523 AQP4 Measured aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 10640.2 12117.8 1.13887
    EXOSC2 Ranked exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] 215.237 230.07 1.06891
    RRM1 Rooted ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 66.377 72.2842 1.08899
    SLC3A1 Squared neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] 53174 44377.4 1.19822
    524 ACY1 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
    AQP5 Measured aquaporin 5. [swissprot;acc:p55064] 10640 12117.6 1.13887
    BRP44 Rooted brain protein 44. [swissprot;acc:o95563] 113.374 123.463 1.08899
    EXOSC3 Ranked exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] 215.237 230.07 1.06891
    525 CPA1 Squared carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 53174 44377.4 1.19822
    EXOSC5 Ranked exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] 215.237 230.07 1.06891
    MIP Measured lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 10639.8 12117.3 1.13887
    SEPT7 Rooted septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 113.374 123.463 1.08899
    526 AQP2 Measured aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 10639.9 12117.4 1.13886
    ETFB Squared electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] 31189.6 37352.8 1.1976
    RRP1 Ranked nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] 250.538 234.401 1.06884
    SEPT6 Rooted septin 6. [swissprot;acc:q14141] 113.169 123.23 1.0889
    527 DDX31 Ranked dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 248.56 232.579 1.06871
    DNASE2B Rooted deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 153.191 166.771 1.08865
    LSM5 Squared u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 18011.9 21552.8 1.19659
    PPM1B Measured protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 4775.11 5438.18 1.13886
    528 AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 10635.3 12111.4 1.13879
    PPP2R1A Squared serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 10606 8868.81 1.19588
    WIPF1 Rooted wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] 66.941 72.7546 1.08685

    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/