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 [...,...].
    Gene Rank description red Hugo Network Comparison Type Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 658 to 707 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		red
    		Hugo
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    83 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 60583.7 NFU1 Squared Low confidence 74280 1.22607
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 88.2482 MAGED4 Ranked High confidence 110.265 1.24949
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 4932.27 FOS Measured 7033.29 1.42597
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 7030.67 DVL1 Low confidence 7794.8 1.10869
    serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 117718 PPP2R5A Squared High confidence 70505.9 1.66962
    serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 63.6507 PPP2R1B Rooted 48.7127 1.30666
    star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] 61.8872 STARD7 Low confidence 67.9229 1.09753
    84 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 117515 BRAF Squared High confidence 70412.3 1.66896
    hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 88.2482 MAGEE2 Ranked 110.265 1.24949
    jun dimerization protein. [refseq;acc:nm_130469] 4932.27 no value Measured 7033.29 1.42597
    nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 46.7419 NFYC Rooted 60.9337 1.30362
    nucleolin (protein c23). [swissprot;acc:p19338] 70162 NCL Squared Low confidence 58112.6 1.20735
    septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 11141.5 SEPT4 Measured 12351.1 1.10857
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 62.4962 no value Rooted 68.5193 1.09638
    226.338 Ranked 207.874 1.08882
    85 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 67438.6 ATG12 Squared High confidence 40697 1.65709
    ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 46.7419 NFYA Rooted 60.9337 1.30362
    dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 61.1174 DFFB Low confidence 66.8946 1.09453
    fos-related antigen 2. [swissprot;acc:p15408] 4941.95 FOSL2 Measured High confidence 7037.11 1.42395
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 88.2482 no value Ranked 110.265 1.24949
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 225.735 KCND2 Low confidence 245.308 1.08671
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 7034.43 DVL2 Measured 7797.14 1.10843
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 60862.1 no value Squared 50419.2 1.20712
    86 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 DFFB Ranked 215.309 1.08645
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 88.2482 MAGEA11 High confidence 110.265 1.24949
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 4942.49 FOSB Measured 7037.32 1.42384
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 66860.1 SEPT7 Squared Low confidence 80573.4 1.2051
    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 PPP2R1A Rooted High confidence 48.8838 1.30146
    transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] 79.2778 BACH1 Low confidence 86.7076 1.09372
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 105500 KRAS Squared High confidence 64146.3 1.64468
    vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] 7263.76 PTPRA Measured Low confidence 8046.29 1.10773
    87 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 APBA1 Rooted High confidence 54.9687 1.30003
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 4944.3 FOSL1 Measured 7038.04 1.42347
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 60811 no value Squared Low confidence 50467.3 1.20496
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 105482 SHOC2 High confidence 64136.9 1.64464
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 88.2482 MAGEA2B Ranked 110.265 1.24949
    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 NFE2L2 Rooted Low confidence 86.7076 1.09372
    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] 225.545 KCND3 Ranked 244.933 1.08596
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 7054.1 DVL3 Measured 7809.38 1.10707
    88 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 60759.9 ATG3 Squared 50515.5 1.2028
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 88.2482 no value Ranked High confidence 110.265 1.24949
    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 KCND1 Low confidence 244.701 1.0855
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 2411.93 KCND2 Measured High confidence 1695.45 1.42259
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 37.3005 PSEN2 Rooted 48.4141 1.29795
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 105482 no value Squared 64137.2 1.64463
    serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] 9631.47 MAK Measured Low confidence 10633 1.10399
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] 79.2778 BACH2 Rooted 86.7076 1.09372
    89 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 187.345 BEST1 204.579 1.09199
    cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 2414.22 CTH Measured High confidence 1698.12 1.4217
    intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] 9623.55 ICK Low confidence 10621.3 1.10368

    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/