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 512 to 561 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    128 STRN striatin. [swissprot;acc:o43815] Divided 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
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 350 290 1.2069
    134 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted 226.884 194.79 32.094
    transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 218.36 205.4 12.96
    DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Divided High confidence 350 290 1.2069
    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 1.06391
    135 CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] High confidence 350 290 1.2069
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted Low confidence 202.96 190.094 12.866
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] High confidence 263.215 231.407 31.808
    TAGLN3 neuronal protein np25. [swissprot;acc:q9ui15] Divided Low confidence 218.66 205.57 1.06368
    136 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Subtracted 219.344 206.52 12.824
    CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided High confidence 350 290 1.2069
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 231.407 31.808
    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 Low confidence 202.996 190.854 1.06362
    137 no value testican-3 precursor. [swissprot;acc:q9bq16] 220.395 234.389 1.0635
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Subtracted High confidence 263.191 231.394 31.797
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Divided 350 290 1.2069
    VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted Low confidence 203.678 190.88 12.798
    138 no value transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Divided 218.36 205.4 1.0631
    ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Subtracted 219.273 206.507 12.766
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Divided High confidence 194.372 234.204 1.20493
    TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Subtracted 174.667 205.556 30.889
    139 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Divided 271.752 225.68 1.20415
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted 287.41 256.835 30.575
    DNAJC8 dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] Low confidence 219.838 207.417 12.421
    SPOCK1 testican-1 precursor (spock protein). [swissprot;acc:q08629] Divided 220.254 234.111 1.06291
    140 GGNBP2 c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] Subtracted 219.838 207.417 12.421
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] High confidence 228.306 198.011 30.295
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Divided 59 49 1.20408
    SPOCK2 testican-2 precursor. [swissprot;acc:q92563] Low confidence 220.222 234.047 1.06278
    141 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 219.344 206.52 1.0621

    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/