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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3501 to 3550 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    876 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Ranked 212.002 203.954 1.03946
    myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Squared 18650.4 21632 1.15987
    nitrogen fixation cluster-like. [refseq;acc:nm_014301] Rooted 84.6378 89.8201 1.06123
    peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Measured 5644.68 6223.23 1.10249
    877 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Ranked 212.002 203.954 1.03946
    mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Measured 5797.88 6391.75 1.10243
    myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Squared 18650.4 21632 1.15987
    star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Rooted 84.6378 89.8201 1.06123
    878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Ranked 212.002 203.954 1.03946
    mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Measured 5797.88 6391.75 1.10243
    star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Rooted 84.6378 89.8201 1.06123
    triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Squared 23242.1 26955.1 1.15975
    879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Ranked 212.002 203.954 1.03946
    ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Squared 23242.1 26955.1 1.15975
    neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Rooted 84.6378 89.8201 1.06123
    nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Measured 5797.88 6391.75 1.10243
    880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Ranked 212.002 203.954 1.03946
    lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Squared 23242.1 26955.1 1.15975
    mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Rooted 84.6378 89.8201 1.06123
    peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Measured 5166.04 5694.55 1.1023
    881 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 5912.84 6517.69 1.10229
    l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Ranked 227.604 219.001 1.03928
    mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Rooted 84.6378 89.8201 1.06123
    seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Squared 23242.1 26955.1 1.15975
    882 n-myc proto-oncogene protein. [swissprot;acc:p04198] Ranked 227.601 219.008 1.03924
    neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Rooted 84.6378 89.8201 1.06123
    seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Squared 23242.1 26955.1 1.15975
    vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Measured 5912.84 6517.69 1.10229
    883 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
    ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Ranked 227.596 219.017 1.03917
    neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Rooted 84.6378 89.8201 1.06123
    parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Squared 18178.2 21081.9 1.15974
    884 ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Ranked 227.596 219.017 1.03917
    hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Squared 18178.2 21081.9 1.15974
    mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Measured 5167.15 5695.44 1.10224
    sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Rooted 84.6378 89.8201 1.06123
    885 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Squared 18178.2 21081.9 1.15974
    junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Rooted 60.6175 64.3272 1.0612
    mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Measured 5168.01 5696.12 1.10219
    nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Ranked 227.596 219.017 1.03917
    886 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018
    pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Squared 18178.2 21081.9 1.15974
    tax interaction protein 1. [refseq;acc:nm_014604] Rooted 60.6175 64.3272 1.0612
    upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Measured 5903.18 6506.32 1.10217
    887 60s ribosomal protein l8. [swissprot;acc:p25120] Squared 18178.2 21081.9 1.15974
    m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Rooted 49.6944 52.7281 1.06105
    transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Measured 5903.18 6506.32 1.10217
    transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Ranked 244.155 234.96 1.03913
    888 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Rooted 56.7827 60.2401 1.06089
    hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Squared 18178.2 21081.9 1.15974

    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
    - 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/