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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 101 to 150 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    101 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 88.2482 110.265 1.24949
    102 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2
    103 trophinin. [swissprot;acc:q12816] TRO
    104 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 252.371 202.016 1.24926
    105 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] GNB1 266.716 333.165 1.24914
    106 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 252.329 202.004 1.24913
    107 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 252.309 201.998 1.24907
    108 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 252.296 201.995 1.24902
    109 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] GNB4 266.933 333.281 1.24856
    110 deltex 2. [refseq;acc:nm_020892] DTX2 333.144 267.393 1.2459
    111 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] DTX1 332.925 267.274 1.24563
    112 t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] PBK 332.874 267.246 1.24557
    113 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3
    114 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1
    115 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2
    116 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] GNB3 268.565 334.483 1.24545
    117 neuralized-like. [refseq;acc:nm_004210] NEURL 332.326 266.948 1.24491
    118 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] NDUFA12 284.753 228.934 1.24382
    119 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 318.982 259.004 1.23157
    120 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 269.278 327.709 1.21699
    121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] CTH 269.254 327.655 1.2169
    122 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 269.248 327.642 1.21688
    123 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] KCND1 269.23 327.601 1.21681
    124 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 208.52 171.595 1.21519
    125 high-mobility group 20a. [refseq;acc:nm_018200] HMG20A 208.588 171.778 1.21429
    126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 94 114 1.21277
    127 putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] CHMP2A
    128 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP
    129 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24
    130 protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A
    131 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] SON 294.053 242.562 1.21228
    132 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 350 290 1.2069
    133 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] TOB1
    134 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP
    135 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4
    136 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3
    137 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2
    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 194.372 234.204 1.20493
    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 271.752 225.68 1.20415
    140 ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA 59 49 1.20408
    141 ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC
    142 ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB
    143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN
    144 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] KCNIP1 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
    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 265.632 319.531 1.20291
    147 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value 50.7983 42.3003 1.2009
    148 sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A 296.677 247.559 1.19841
    149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value 142 170 1.19718
    150 myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B 55 46 1.19565

    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/