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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1358 to 1407 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    85 Subtracted RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Measured High confidence 21370.8 3474.3 17896.5
    SLC7A7 y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Rooted Low confidence 68.7629 6.7248 75.4877
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Ranked High confidence 296.677 49.118 247.559
    86 Divided BACH1 transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Rooted Low confidence 79.2778 1.09372 86.7076
    DFFB dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Ranked 233.922 1.08645 215.309
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Measured High confidence 4942.49 1.42384 7037.32
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Squared 105500 1.64468 64146.3
    MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Ranked 88.2482 1.24949 110.265
    PPP2R1A 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] Rooted 63.6205 1.30146 48.8838
    PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Measured Low confidence 7263.76 1.10773 8046.29
    SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 66860.1 1.2051 80573.4
    Subtracted BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 81989.8 10079 71910.8
    DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Ranked High confidence 335 49 286
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Rooted 40.3361 16.0411 24.295
    MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Measured Low confidence 11285.3 966.8 10318.5
    PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] High confidence 21370.8 3474.3 17896.5
    ROGDI leucine zipper domain protein. [refseq;acc:nm_024589] Ranked Low confidence 221.996 16.824 238.82
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Squared High confidence 103496 43352 146848
    SLC7A11 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Rooted Low confidence 68.7629 6.7248 75.4877
    87 Divided no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared 60811 1.20496 50467.3
    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] Rooted High confidence 42.2825 1.30003 54.9687
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Measured Low confidence 7054.1 1.10707 7809.38
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] High confidence 4944.3 1.42347 7038.04
    KCND3 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] Ranked Low confidence 225.545 1.08596 244.933
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] High confidence 88.2482 1.24949 110.265
    NFE2L2 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] Rooted Low confidence 79.2778 1.09372 86.7076
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Squared High confidence 105482 1.64464 64136.9
    Subtracted ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 103496 43352 146848
    CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Low confidence 81761.4 10031.2 71730.2
    DGKQ diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Ranked 229.556 16.1 213.456
    GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Rooted High confidence 40.3362 16.0408 24.2954
    MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured Low confidence 11285.3 966.8 10318.5
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] High confidence 20287.2 3203.4 17083.8
    RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Ranked 249.663 48.6 298.263
    SLC7A6 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Rooted Low confidence 68.7629 6.7248 75.4877
    88 Divided no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Ranked High confidence 88.2482 1.24949 110.265
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Squared 105482 1.64463 64137.2
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence 60759.9 1.2028 50515.5
    BACH2 transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Rooted 79.2778 1.09372 86.7076
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked 225.428 1.0855 244.701
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured High confidence 2411.93 1.42259 1695.45
    MAK serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Low confidence 9631.47 1.10399 10633
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted High confidence 37.3005 1.29795 48.4141
    Subtracted no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 40.3364 16.0396 24.2968
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared 98517.9 41590.7 56927.2
    CPD carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Ranked Low confidence 16 16 32
    EIF4B eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Rooted 68.7629 6.7248 75.4877
    HAAO 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Squared 65044.3 9918 74962.3
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Measured High confidence 16074 3185.6 12888.4
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Low confidence 11285.3 966.8 10318.5

    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/