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 network_comparison green
    Results: HTML CSV LaTeX Showing element 108 to 157 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		network_comparison
    		green
    108 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 252.296 1.24902 201.995
    109 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] GNB4 266.933 1.24856 333.281
    110 deltex 2. [refseq;acc:nm_020892] DTX2 333.144 1.2459 267.393
    111 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] DTX1 332.925 1.24563 267.274
    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 1.24557 267.246
    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 1.24545 334.483
    117 neuralized-like. [refseq;acc:nm_004210] NEURL 332.326 1.24491 266.948
    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 1.24382 228.934
    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 1.23157 259.004
    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 1.21699 327.709
    121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] CTH 269.254 1.2169 327.655
    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 1.21688 327.642
    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 1.21681 327.601
    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 1.21519 171.595
    125 high-mobility group 20a. [refseq;acc:nm_018200] HMG20A 208.588 1.21429 171.778
    126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 94 1.21277 114
    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 1.21228 242.562
    132 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 350 1.2069 290
    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 1.20493 234.204
    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 1.20415 225.68
    140 ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA 59 1.20408 49
    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 1.20312 319.651
    145 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] KCNIP4 265.639 1.20293 319.546
    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 1.20291 319.531
    147 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value 50.7983 1.2009 42.3003
    148 sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A 296.677 1.19841 247.559
    149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value 142 1.19718 170
    150 myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B 55 1.19565 46
    151 myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C
    152 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] no value
    153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] RBM15B 249.663 1.19466 298.263
    154 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] RGS19
    155 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] RBM15
    156 regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] RGS20
    157 transcription factor lbx1. [swissprot;acc:p52954] LBX1

    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/