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 482 to 531 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    121 DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Divided Low confidence 203.007 189.985 1.06854
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted High confidence 227.202 192.823 34.379
    VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Low confidence 203.914 190.189 13.725
    122 no value nanos (fragment). [sptrembl;acc:q8wy41] Divided 203.66 217.479 1.06785
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Subtracted High confidence 199.949 234.187 34.238
    KCND3 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] Divided 269.248 327.642 1.21688
    VPS18 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Subtracted Low confidence 204.161 190.791 13.37
    123 DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided 202.96 190.094 1.06768
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] High confidence 269.23 327.601 1.21681
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 227.032 193.056 33.976
    STRN striatin. [swissprot;acc:o43815] Low confidence 214.085 200.796 13.289
    124 DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 220.268 206.997 13.271
    HMG20B 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 High confidence 208.52 171.595 1.21519
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 285.684 252.234 33.45
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Divided Low confidence 224.763 210.566 1.06742
    125 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 213.243 227.616 1.0674
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] High confidence 208.588 171.778 1.21429
    PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Subtracted Low confidence 220.268 206.997 13.271
    SKP1A 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] High confidence 285.684 252.234 33.45
    126 FBXW7 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]
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided Low confidence 191.688 179.639 1.06707
    NDUFS4 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 226.892 213.661 13.231
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided High confidence 94 114 1.21277
    127 APC adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] Subtracted Low confidence 222.31 235.538 13.228
    CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided High confidence 94 114 1.21277
    CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Subtracted 285.684 252.234 33.45
    VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Divided Low confidence 203.678 190.88 1.06705
    128 APC2 adenomatous polyposis coli like. [refseq;acc:nm_005883] Subtracted 222.34 235.547 13.207
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] High confidence 285.684 252.234 33.45
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided 94 114 1.21277
    STRN striatin. [swissprot;acc:o43815] Low confidence 214.085 200.796 1.06618
    129 COL4A3BP 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] 220.969 235.572 1.06609
    CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted High confidence 285.684 252.234 33.45
    TAGLN transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Low confidence 218.561 205.431 13.13
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Divided High confidence 94 114 1.21277
    130 ABRA striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Low confidence 225.495 211.529 1.06602
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] High confidence 94 114 1.21277
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Subtracted 242.735 276.059 33.324
    TAGLN3 neuronal protein np25. [swissprot;acc:q9ui15] Low confidence 218.66 205.57 13.09
    131 EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] High confidence 242.718 276.018 33.3
    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] Divided 294.053 242.562 1.21228
    STRN4 striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 213.878 200.825 1.065
    Subtracted 13.053
    132 DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Divided 220.268 206.997 1.06411
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted 203.016 189.965 13.051
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] High confidence 229.406 196.695 32.711
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided 350 290 1.2069
    133 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 226.887 194.72 32.167
    DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence 203.007 189.985 13.022
    PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Divided 220.268 206.997 1.06411

    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/