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 description Gene Value Type Hugo Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 262 to 311 of 16578 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    131 striatin 4 (zinedin). [swissprot;acc:q9nrl3] STRN4 Low confidence 213.878 200.825 1.065
    132 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] DAZAP1 220.268 206.997 1.06411
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 High confidence 350 290 1.2069
    133 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] PROM1 Low confidence 220.268 206.997 1.06411
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] TOB1 High confidence 350 290 1.2069
    134 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP
    transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] TAGLN Low confidence 218.561 205.431 1.06391
    135 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 High confidence 350 290 1.2069
    neuronal protein np25. [swissprot;acc:q9ui15] TAGLN3 Low confidence 218.66 205.57 1.06368
    136 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 High confidence 350 290 1.2069
    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] HMG20B Low confidence 202.996 190.854 1.06362
    137 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 High confidence 350 290 1.2069
    testican-3 precursor. [swissprot;acc:q9bq16] no value Low confidence 220.395 234.389 1.0635
    138 serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] PPP2CA High confidence 194.372 234.204 1.20493
    transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] no value Low confidence 218.36 205.4 1.0631
    139 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] APBA1 High confidence 271.752 225.68 1.20415
    testican-1 precursor (spock protein). [swissprot;acc:q08629] SPOCK1 Low confidence 220.254 234.111 1.06291
    140 ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA High confidence 59 49 1.20408
    testican-2 precursor. [swissprot;acc:q92563] SPOCK2 Low confidence 220.222 234.047 1.06278
    141 ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC High confidence 59 49 1.20408
    rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] ARHGEF7 Low confidence 219.344 206.52 1.0621
    142 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] MAN1B1 211.056 198.732 1.06201
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB High confidence 59 49 1.20408
    143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] PSEN2 Low confidence 211.056 198.732 1.06201
    144 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] FBXW7
    kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] KCNIP1 High confidence 265.686 319.651 1.20312
    145 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] KCNIP4 265.639 319.546 1.20293
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 Low confidence 211.056 198.732 1.06201
    146 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] KCNIP2 High confidence 265.632 319.531 1.20291
    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] NDUFS4 Low confidence 226.892 213.661 1.06193
    147 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value High confidence 50.7983 42.3003 1.2009
    rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] ARHGEF6 Low confidence 219.273 206.507 1.06182
    148 sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A High confidence 296.677 247.559 1.19841
    sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] SENP8 Low confidence 210.579 198.33 1.06176
    149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value High confidence 142 170 1.19718
    ubiquitin-like protein nedd8. [swissprot;acc:q15843] NEDD8 Low confidence 210.579 198.33 1.06176
    150 myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B High confidence 55 46 1.19565
    serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] PLK1 Low confidence 206.516 194.554 1.06148
    151 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] CTSZ
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C High confidence 55 46 1.19565
    152 high-mobility group 20a. [refseq;acc:nm_018200] HMG20A Low confidence 202.934 191.187 1.06144
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] no value High confidence 55 46 1.19565
    153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] RBM15B 249.663 298.263 1.19466
    rab11-family interacting protein 4. [refseq;acc:nm_032932] RAB11FIP4 Low confidence 183.27 172.702 1.06119
    154 eferin. [swissprot;acc:o75154] RAB11FIP3
    regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] RGS19 High confidence 249.663 298.263 1.19466
    155 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] CTSL2 Low confidence 211.818 199.734 1.0605
    putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] RBM15 High confidence 249.663 298.263 1.19466
    156 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] CTSL1 Low confidence 211.808 199.761 1.06031

    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/