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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2030 to 2079 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    508 autoantigen ngp-1. [swissprot;acc:q13823] Rooted 49.4756 53.9896 1.09124
    leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Squared 23512.2 28206.2 1.19964
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Ranked 177.698 190.24 1.07058
    509 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Measured 7551.8 8630.06 1.14278
    60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Rooted 50.2583 46.057 1.09122
    carboxypeptidase b precursor. [refseq;acc:nm_020361] Ranked 177.698 190.239 1.07057
    dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Squared 23512.2 28206.2 1.19964
    510 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Measured 5975.11 6826.24 1.14245
    plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Ranked 177.699 190.24 1.07057
    protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Rooted 149.397 136.972 1.09071
    transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Squared 17281.7 20723 1.19913
    511 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]
    proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Ranked 250.053 233.725 1.06986
    serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Measured 5975.11 6826.24 1.14245
    suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Rooted 50.5979 46.392 1.09066
    512 block of proliferation 1. [swissprot;acc:q14137] Ranked 250.794 234.433 1.06979
    cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 19987.6 23960.7 1.19878
    protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Rooted 56.3798 61.4858 1.09056
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Measured 10807.4 12338.5 1.14167
    513 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 7485.08 8543.66 1.14143
    60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Rooted 51.5881 47.3127 1.09036
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked 218.596 204.344 1.06975
    transforming protein rhoc (h9). [swissprot;acc:p08134] Squared 19987.6 23960.7 1.19878
    514 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Measured 7477 8532.02 1.1411
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Ranked 218.613 204.382 1.06963
    thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Squared 19987.6 23960.7 1.19878
    xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Rooted 58.7805 64.0772 1.09011
    515 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Squared 19987.6 23960.7 1.19878
    pescadillo homolog 1. [swissprot;acc:o00541] Ranked 251.297 234.941 1.06962
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Measured 3890.53 4439.07 1.14099
    u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Rooted 56.3551 61.4322 1.09009
    516 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 50.7935 46.6042 1.08989
    n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Measured 4910.6 5600.61 1.14051
    transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 19987.6 23960.7 1.19878
    u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 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] 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] Measured 4910.6 5600.61 1.14051
    metaxin 2. [swissprot;acc:o75431] 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] Squared 19263.3 23092.3 1.19877
    518 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Ranked 250.858 234.563 1.06947
    proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Squared 11447.3 13719.2 1.19847
    trinucleotide repeat containing 15. [refseq;acc:nm_015575] Rooted 50.0578 54.5502 1.08974
    udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Measured 4910.6 5600.61 1.14051
    519 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 9648.27 10994.9 1.13957
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Squared 22387.1 26827.3 1.19834
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Ranked 218.702 204.582 1.06902
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Rooted 114.309 124.527 1.08939
    520 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 61.1902 66.6503 1.08923
    endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Measured 9642.22 10986.4 1.13941
    paxillin. [swissprot;acc:p49023] Squared 22387.1 26827.3 1.19834

    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/