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 80 to 129 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    40 SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Low confidence 255.382 223.538 1.14245
    41 no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] High confidence 322 253 1.27273
    GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Low confidence 228.147 200.55 1.13761
    42 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] High confidence 204.641 160.957 1.2714
    GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Low confidence 227.371 200.532 1.13384
    43 no value jun dimerization protein. [refseq;acc:nm_130469] High confidence 204.641 160.957 1.2714
    RGS12 regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Low confidence 247.768 219.841 1.12703
    44 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] High confidence 204.641 161.046 1.2707
    PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Low confidence 242.742 217.217 1.11751
    45 FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence 204.641 161.051 1.27066
    MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Low confidence 242.742 217.217 1.11751
    46 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] High confidence 204.642 161.068 1.27053
    PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Low confidence 242.742 217.217 1.11751
    47 FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
    TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] High confidence 325.586 256.492 1.26938
    48 no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Low confidence 242.742 217.217 1.11751
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 65.4586 83.0461 1.26868
    49 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 133 105 1.26667
    TBX19 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Low confidence 225.438 202.569 1.11289
    50 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] High confidence 133 105 1.26667
    JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Low confidence 234.802 260.98 1.11149
    51 JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] High confidence 133 105 1.26667
    52 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
    SMPD2 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Low confidence 234.802 260.98 1.11149
    53 JUNB transcription factor jun-b. [swissprot;acc:p17275] High confidence 201.144 158.868 1.26611
    TMEM33 db83 protein. [swissprot;acc:p57088] Low confidence 234.802 260.98 1.11149
    54 CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 267.448 240.822 1.11056
    JUND transcription factor jun-d. [swissprot;acc:p17535] High confidence 200.941 158.941 1.26425
    55 CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Low confidence 267.376 240.78 1.11046
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] High confidence 320.927 254.434 1.26134
    56 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 266.856 336.233 1.25998
    T brachyury protein (t protein). [swissprot;acc:o15178] Low confidence 224.922 202.592 1.11022
    57 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 202.802 182.73 1.10985
    GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] High confidence 266.856 336.233 1.25998
    58 no value jun dimerization protein. [refseq;acc:nm_130469] Low confidence 202.802 182.73 1.10985
    GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] High confidence 266.863 336.191 1.25979
    59 GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 336.19 1.25978
    NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Low confidence 233.134 210.267 1.10875
    60 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] 202.793 182.961 1.10839
    GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 266.864 336.184 1.25976
    61 FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Low confidence 202.792 182.974 1.10831
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence 266.864 336.182 1.25975
    62 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Low confidence 202.79 183.017 1.10804
    GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] High confidence 266.865 336.181 1.25974
    63 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 336.178 1.25973
    RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Low confidence 265.688 239.902 1.10749
    64 GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] High confidence 266.868 336.159 1.25965
    JUND transcription factor jun-d. [swissprot;acc:p17535] Low confidence 202.709 183.361 1.10552
    65 GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] High confidence 267.136 336.077 1.25807

    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/