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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2025 to 2074 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    507 ANLN Rooted anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 144.606 157.824 1.09141
    CBL Measured cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 6875.08 7858.38 1.14302
    NPEPPS Squared puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] 23512.2 28206.2 1.19964
    WDR12 Ranked wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 251.299 234.729 1.07059
    508 AGPAT2 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 7556.75 8636.87 1.14293
    CPA3 Ranked mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 177.698 190.24 1.07058
    GNL2 Rooted autoantigen ngp-1. [swissprot;acc:q13823] 49.4756 53.9896 1.09124
    LTA4H Squared leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] 23512.2 28206.2 1.19964
    509 no value Measured 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] 7551.8 8630.06 1.14278
    CPA6 Ranked carboxypeptidase b precursor. [refseq;acc:nm_020361] 177.698 190.239 1.07057
    DHODH Squared dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] 23512.2 28206.2 1.19964
    MRPL11 Rooted 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 50.2583 46.057 1.09122
    510 BRF1 Squared 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] 17281.7 20723 1.19913
    CPB2 Ranked plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 177.699 190.24 1.07057
    GRB2 Measured growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 5975.11 6826.24 1.14245
    PPP1R7 Rooted protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 149.397 136.972 1.09071
    511 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 50.5979 46.392 1.09066
    NEK2 Measured 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] 5975.11 6826.24 1.14245
    NOL1 Ranked proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 250.053 233.725 1.06986
    NOLA1 Squared nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 17281.7 20723 1.19913
    512 no value Measured small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 10807.4 12338.5 1.14167
    BOP1 Ranked block of proliferation 1. [swissprot;acc:q14137] 250.794 234.433 1.06979
    CBS Squared cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 19987.6 23960.7 1.19878
    PPM1B Rooted protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 56.3798 61.4858 1.09056
    513 AGPAT3 Measured 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
    DVL1 Ranked segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 218.596 204.344 1.06975
    RHOC Squared transforming protein rhoc (h9). [swissprot;acc:p08134] 19987.6 23960.7 1.19878
    RPL4 Rooted 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 51.5881 47.3127 1.09036
    514 AGPAT4 Measured 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] 7477 8532.02 1.1411
    DVL2 Ranked segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 218.613 204.382 1.06963
    TST Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 19987.6 23960.7 1.19878
    XAB2 Rooted xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 58.7805 64.0772 1.09011
    515 no value Measured transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 3890.53 4439.07 1.14099
    LSM1 Rooted u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 56.3551 61.4322 1.09009
    MPST Squared 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 19987.6 23960.7 1.19878
    PES1 Ranked pescadillo homolog 1. [swissprot;acc:o00541] 251.297 234.941 1.06962
    516 AK2 Rooted adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 50.7935 46.6042 1.08989
    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

    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/