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 description Value Type 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
    		description
    		Value Type
    		red
    		green
    		network_comparison
    507 ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Rooted 144.606 157.824 1.09141
    CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Measured 6875.08 7858.38 1.14302
    NPEPPS puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Squared 23512.2 28206.2 1.19964
    WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Ranked 251.299 234.729 1.07059
    508 AGPAT2 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] Measured 7556.75 8636.87 1.14293
    CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Ranked 177.698 190.24 1.07058
    GNL2 autoantigen ngp-1. [swissprot;acc:q13823] Rooted 49.4756 53.9896 1.09124
    LTA4H 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
    509 no value 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
    CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Ranked 177.698 190.239 1.07057
    DHODH dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Squared 23512.2 28206.2 1.19964
    MRPL11 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Rooted 50.2583 46.057 1.09122
    510 BRF1 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
    CPB2 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
    GRB2 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
    PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Rooted 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 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
    NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Ranked 250.053 233.725 1.06986
    NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Squared 17281.7 20723 1.19913
    512 no value small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Measured 10807.4 12338.5 1.14167
    BOP1 block of proliferation 1. [swissprot;acc:q14137] Ranked 250.794 234.433 1.06979
    CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 19987.6 23960.7 1.19878
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Rooted 56.3798 61.4858 1.09056
    513 AGPAT3 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] Measured 7485.08 8543.66 1.14143
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked 218.596 204.344 1.06975
    RHOC transforming protein rhoc (h9). [swissprot;acc:p08134] Squared 19987.6 23960.7 1.19878
    RPL4 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Rooted 51.5881 47.3127 1.09036
    514 AGPAT4 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
    DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Ranked 218.613 204.382 1.06963
    TST thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Squared 19987.6 23960.7 1.19878
    XAB2 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Rooted 58.7805 64.0772 1.09011
    515 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Measured 3890.53 4439.07 1.14099
    LSM1 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
    MPST 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Squared 19987.6 23960.7 1.19878
    PES1 pescadillo homolog 1. [swissprot;acc:o00541] Ranked 251.297 234.941 1.06962
    516 AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Rooted 50.7935 46.6042 1.08989
    GALK2 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Measured 4910.6 5600.61 1.14051
    LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Ranked 228.255 213.422 1.0695
    RHOA transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 19987.6 23960.7 1.19878
    517 no value 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
    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
    EIF3I 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
    MTX2 metaxin 2. [swissprot;acc:o75431] Ranked 219.537 234.793 1.06949
    518 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] Rooted 50.0578 54.5502 1.08974
    GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Measured 4910.6 5600.61 1.14051
    GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Ranked 250.858 234.563 1.06947
    PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Squared 11447.3 13719.2 1.19847
    519 DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Ranked 218.702 204.582 1.06902
    GYS1 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Measured 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/