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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 475 to 524 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    119 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Divided SLC11A1 Low confidence 225.666 211.107 1.06897
    testican-2 precursor. [swissprot;acc:q92563] Subtracted SPOCK2 220.222 234.047 13.825
    120 nanos (fragment). [sptrembl;acc:q8wy41] no value 203.66 217.479 13.819
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 High confidence 227.199 192.715 34.484
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided KCND2 269.278 327.709 1.21699
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 Low confidence 203.016 189.965 1.0687
    121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] CTH High confidence 269.254 327.655 1.2169
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted TIAL1 227.202 192.823 34.379
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Divided DVL2 Low confidence 203.007 189.985 1.06854
    vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Subtracted VPS33A 203.914 190.189 13.725
    122 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 High confidence 199.949 234.187 34.238
    nanos (fragment). [sptrembl;acc:q8wy41] Divided no value Low confidence 203.66 217.479 1.06785
    potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] KCND3 High confidence 269.248 327.642 1.21688
    vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Subtracted VPS18 Low confidence 204.161 190.791 13.37
    123 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided KCND1 High confidence 269.23 327.601 1.21681
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 Low confidence 202.96 190.094 1.06768
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted SNRPD1 High confidence 227.032 193.056 33.976
    striatin. [swissprot;acc:o43815] STRN Low confidence 214.085 200.796 13.289
    124 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] DAZAP1 220.268 206.997 13.271
    high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided HMG20B High confidence 208.52 171.595 1.21519
    natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] SLC11A2 Low confidence 224.763 210.566 1.06742
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted PSEN2 High confidence 285.684 252.234 33.45
    125 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Divided B9D1 Low confidence 213.243 227.616 1.0674
    high-mobility group 20a. [refseq;acc:nm_018200] HMG20A High confidence 208.588 171.778 1.21429
    prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Subtracted PROM1 Low confidence 220.268 206.997 13.271
    s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] SKP1A High confidence 285.684 252.234 33.45
    126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided STAMBPL1 94 114 1.21277
    f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Subtracted FBXW7 285.684 252.234 33.45
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided LASS2 Low confidence 191.688 179.639 1.06707
    nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted NDUFS4 226.892 213.661 13.231
    127 adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] APC 222.31 235.538 13.228
    cullin homolog 2 (cul-2). [swissprot;acc:q13617] CUL2 High confidence 285.684 252.234 33.45
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided CHMP2A 94 114 1.21277
    vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] VPS33B Low confidence 203.678 190.88 1.06705
    128 adenomatous polyposis coli like. [refseq;acc:nm_005883] Subtracted APC2 222.34 235.547 13.207
    associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided STAMBP High confidence 94 114 1.21277
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted PSEN1 285.684 252.234 33.45
    striatin. [swissprot;acc:o43815] Divided STRN Low confidence 214.085 200.796 1.06618
    129 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted CUL1 High confidence 285.684 252.234 33.45
    goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Divided COL4A3BP Low confidence 220.969 235.572 1.06609
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 High confidence 94 114 1.21277
    transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Subtracted TAGLN Low confidence 218.561 205.431 13.13
    130 neuronal protein np25. [swissprot;acc:q9ui15] TAGLN3 218.66 205.57 13.09
    palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] EGFL8 High confidence 242.735 276.059 33.324
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided CHMP4A 94 114 1.21277
    striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] ABRA Low confidence 225.495 211.529 1.06602
    131 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Subtracted EGFL7 High confidence 242.718 276.018 33.3
    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] Divided SON 294.053 242.562 1.21228
    striatin 4 (zinedin). [swissprot;acc:q9nrl3] STRN4 Low confidence 213.878 200.825 1.065
    Subtracted 13.053

    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/