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