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 258 to 307 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    129 VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 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
    131 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] 294.053 242.562 1.21228
    STRN4 striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 213.878 200.825 1.065
    132 DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 220.268 206.997 1.06411
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence 350 290 1.2069
    133 PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Low confidence 220.268 206.997 1.06411
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 350 290 1.2069
    134 DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
    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
    TAGLN3 neuronal protein np25. [swissprot;acc:q9ui15] Low confidence 218.66 205.57 1.06368
    136 CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] High confidence 350 290 1.2069
    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] Low confidence 202.996 190.854 1.06362
    137 no value testican-3 precursor. [swissprot;acc:q9bq16] 220.395 234.389 1.0635
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] High confidence 350 290 1.2069
    138 no value transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 218.36 205.4 1.0631
    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] High confidence 194.372 234.204 1.20493
    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] 271.752 225.68 1.20415
    SPOCK1 testican-1 precursor (spock protein). [swissprot;acc:q08629] Low confidence 220.254 234.111 1.06291
    140 RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] High confidence 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
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] High confidence 59 49 1.20408
    142 MAN1B1 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] Low confidence 211.056 198.732 1.06201
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] High confidence 59 49 1.20408
    143 ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Low confidence 211.056 198.732 1.06201
    144 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]
    KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 265.686 319.651 1.20312
    145 KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 1.20293
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence 211.056 198.732 1.06201
    146 KCNIP2 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] High confidence 265.632 319.531 1.20291
    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] Low confidence 226.892 213.661 1.06193
    147 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence 50.7983 42.3003 1.2009
    ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 219.273 206.507 1.06182
    148 SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 210.579 198.33 1.06176
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] High confidence 296.677 247.559 1.19841
    149 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Low confidence 210.579 198.33 1.06176
    150 MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence 55 46 1.19565
    PLK1 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Low confidence 206.516 194.554 1.06148
    151 CTSZ cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]
    MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence 55 46 1.19565
    152 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Low confidence 202.934 191.187 1.06144
    153 RAB11FIP4 rab11-family interacting protein 4. [refseq;acc:nm_032932] 183.27 172.702 1.06119
    RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] High confidence 249.663 298.263 1.19466
    154 RAB11FIP3 eferin. [swissprot;acc:o75154] Low confidence 183.27 172.702 1.06119

    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/