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 Network Comparison Type Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1362 to 1411 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    86 BCL6B Subtracted Squared b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Low confidence 81989.8 71910.8 10079
    DFFB Divided Ranked dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 233.922 215.309 1.08645
    DGCR14 Subtracted dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] High confidence 335 286 49
    FOSB Divided Measured protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 4942.49 7037.32 1.42384
    GNG5 Subtracted Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 40.3361 24.295 16.0411
    KRAS Divided Squared transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 105500 64146.3 1.64468
    MAGEA11 Ranked melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 88.2482 110.265 1.24949
    MAGEA9 Subtracted Measured melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Low confidence 11285.3 10318.5 966.8
    PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] High confidence 21370.8 17896.5 3474.3
    PPP2R1A Divided Rooted serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 63.6205 48.8838 1.30146
    PTPRA Measured vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Low confidence 7263.76 8046.29 1.10773
    ROGDI Subtracted Ranked leucine zipper domain protein. [refseq;acc:nm_024589] 221.996 238.82 16.824
    RRAGB Squared ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] High confidence 103496 146848 43352
    SEPT7 Divided septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Low confidence 66860.1 80573.4 1.2051
    SLC7A11 Subtracted Rooted cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] 68.7629 75.4877 6.7248
    87 no value Divided Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 60811 50467.3 1.20496
    ANLN Subtracted anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] High confidence 103496 146848 43352
    APBA1 Divided Rooted 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] 42.2825 54.9687 1.30003
    CTBP2 Subtracted Squared c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Low confidence 81761.4 71730.2 10031.2
    DGKQ Ranked diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] 229.556 213.456 16.1
    DVL3 Divided Measured segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 7054.1 7809.38 1.10707
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] High confidence 4944.3 7038.04 1.42347
    GNG10 Subtracted Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 40.3362 24.2954 16.0408
    KCND3 Divided Ranked 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] Low confidence 225.545 244.933 1.08596
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] High confidence 88.2482 110.265 1.24949
    MAGEA8 Subtracted Measured melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Low confidence 11285.3 10318.5 966.8
    NFE2L2 Divided Rooted nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] 79.2778 86.7076 1.09372
    PCF11 Subtracted Measured pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] High confidence 20287.2 17083.8 3203.4
    RBM15B Ranked chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 249.663 298.263 48.6
    SHOC2 Divided Squared leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 105482 64136.9 1.64464
    SLC7A6 Subtracted Rooted solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence 68.7629 75.4877 6.7248
    88 no value Divided Ranked hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] High confidence 88.2482 110.265 1.24949
    Squared ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 105482 64137.2 1.64463
    Subtracted ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 98517.9 56927.2 41590.7
    Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 40.3364 24.2968 16.0396
    ATG3 Divided Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence 60759.9 50515.5 1.2028
    BACH2 Rooted transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] 79.2778 86.7076 1.09372
    CPD Subtracted Ranked carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 16 32 16
    EIF4B Rooted eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] 68.7629 75.4877 6.7248
    HAAO Squared 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 65044.3 74962.3 9918
    KCND1 Divided Ranked potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 225.428 244.701 1.0855
    KCND2 Measured potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 2411.93 1695.45 1.42259
    KRAS Subtracted transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 16074 12888.4 3185.6
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Low confidence 11285.3 10318.5 966.8
    MAK Divided serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] 9631.47 10633 1.10399
    PSEN2 Rooted presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] High confidence 37.3005 48.4141 1.29795
    RGS19 Subtracted Ranked regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 249.663 298.263 48.6
    89 BEST1 Divided Rooted bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 187.345 204.579 1.09199
    CTH Measured cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] High confidence 2414.22 1698.12 1.4217
    GNG11 Subtracted Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 40.3372 24.3043 16.0329

    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/