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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1912 to 1961 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    239 Rooted u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] SNRPA1 Low confidence 1.05755 71.0859 75.1771
    240 Measured mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 High confidence 1.23071 7711.36 6265.79
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Low confidence 1.06425 7671.08 8163.95
    Ranked androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] AIG1 High confidence 1.11785 227.357 254.15
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value Low confidence 1.04682 162.755 155.476
    Squared c-ets-1 protein (p54). [swissprot;acc:p14921] ETS1 1.09465 52929.8 48353.2
    mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] MAPK14 High confidence 1.31573 42411.6 55802.1
    Rooted ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] no value Low confidence 1.05753 71.0869 75.1768
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 High confidence 1.13758 137.446 120.823
    241 Measured glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] GNPDA2 Low confidence 1.06356 4585.58 4311.52
    plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 High confidence 1.23071 7711.31 6265.76
    Ranked atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] ATP5F1 1.11785 227.357 254.15
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Low confidence 1.04682 162.755 155.476
    Squared atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] ATP5F1 1.09465 52929.8 48353.2
    neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] CHRNA4 High confidence 1.31573 42411.6 55802.1
    Rooted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 1.13758 137.446 120.823
    spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] no value Low confidence 1.05748 72.5948 76.7678
    242 Measured glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] GNPDA1 1.06356 4585.58 4311.52
    max protein. [swissprot;acc:p25912] MAX High confidence 1.22943 4640.26 5704.87
    Ranked homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Low confidence 1.04682 162.755 155.476
    j domain containing protein 1. [swissprot;acc:q9ukb3] DNAJC12 High confidence 1.11785 227.357 254.15
    Squared neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] CHRNA3 1.31573 42411.6 55802.1
    tubulin alpha-8 chain (alpha-tubulin 8). [swissprot;acc:q9ny65] no value Low confidence 1.09454 46646.5 42617.6
    Rooted melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 High confidence 1.13758 137.446 120.823
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Low confidence 1.05744 71.0451 75.1259
    243 Measured dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] DDX39 1.06338 7648.9 8133.69
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 High confidence 1.22652 4246.95 5208.98
    Ranked homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Low confidence 1.04682 162.755 155.476
    sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] SNX13 High confidence 1.11785 227.357 254.15
    Squared sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] SPHK2 1.31573 42411.6 55802.1
    valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] VARS Low confidence 1.09426 51669.9 47219.1
    Rooted anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] ANAPC10 1.05726 67.7543 71.6341
    trophinin. [swissprot;acc:q12816] TRO High confidence 1.13758 137.446 120.823
    244 Measured protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] PPP1R12B Low confidence 1.06331 8759.92 9314.48
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 High confidence 1.22614 4250.14 5211.25
    Ranked ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 1.11785 227.357 254.15
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Low confidence 1.04682 162.755 155.476
    Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] NCBP2L High confidence 1.31245 14728.8 19330.8
    tubulin alpha-1 chain (alpha-tubulin 1). [swissprot;acc:p05209] TUBA1A Low confidence 1.09401 46639.3 42631.6
    Rooted myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B High confidence 1.13683 146.94 167.046
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Low confidence 1.05723 86.9838 91.9621
    245 Measured homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 High confidence 1.22595 4251.65 5212.33
    tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] TP63 Low confidence 1.06313 8509.99 9047.26
    Ranked homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 1.04682 162.755 155.476
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 High confidence 1.11751 226.109 202.333
    Squared 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 1.31131 8875.01 6768.05
    tubulin alpha-6 chain (alpha-tubulin 6). [swissprot;acc:q9bqe3] TUBA1C Low confidence 1.0937 46635.1 42639.6
    Rooted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C High confidence 1.13683 146.94 167.046
    probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] ATP2C2 Low confidence 1.05715 65.9913 69.763
    246 Measured homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 High confidence 1.22583 4252.66 5213.05

    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/