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 2551 to 2600 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    638 sorting nexin 17. [swissprot;acc:q15036] Ranked 228.639 242.258 1.05957
    transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Rooted 60.0129 64.7371 1.07872
    639 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Squared 17618.8 20776.8 1.17924
    delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Rooted 60.0129 64.7371 1.07872
    nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Ranked 217.67 230.596 1.05938
    nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Measured 7753.59 8728.13 1.12569
    640 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Rooted 60.0129 64.7371 1.07872
    glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Measured 4811.02 5414.64 1.12547
    intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Ranked 217.67 230.596 1.05938
    nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Squared 22848.5 26941.5 1.17914
    641 peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Measured 4810.85 5414.21 1.12542
    pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Ranked 217.67 230.596 1.05938
    synapsin i (brain protein 4.1). [swissprot;acc:p17600] Rooted 60.0129 64.7371 1.07872
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Squared 18364.9 21653.8 1.17909
    642 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 16123.9 19009.7 1.17898
    atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Measured 4810.85 5414.23 1.12542
    intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Ranked 217.67 230.596 1.05938
    ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Rooted 64.4857 69.5606 1.0787
    643 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] Squared 16126.5 19012.6 1.17897
    autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Rooted 87.4586 81.0798 1.07867
    hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Ranked 217.67 230.596 1.05938
    polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Measured 4810.85 5414.23 1.12542
    644 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Squared 16156.3 19046 1.17886
    cgthba protein (-14 gene protein). [swissprot;acc:q12980] Ranked 217.67 230.596 1.05938
    cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Measured 4810.85 5414.22 1.12542
    rna polymerase i associated factor 53. [refseq;acc:nm_022490] Rooted 51.1896 47.4617 1.07855
    645 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Measured 4810.71 5413.89 1.12538
    hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Ranked 217.67 230.596 1.05938
    nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Squared 22722.5 26786.5 1.17885
    preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Rooted 63.1463 68.1044 1.07852
    646 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Squared 27898 32866.2 1.17808
    dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Rooted 63.1463 68.1044 1.07852
    fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Measured 4019.88 4522.61 1.12506
    short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Ranked 216.731 229.549 1.05914
    647 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Rooted 64.5657 69.6237 1.07834
    cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Squared 33384.2 39324.9 1.17795
    dynein light chain 2. [refseq;acc:nm_080677] Ranked 216.731 229.549 1.05914
    short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Measured 5167.88 4594.43 1.12481
    648 methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Ranked 218.227 206.078 1.05895
    retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Squared 29174 34363.5 1.17788
    splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Measured 5248.07 5901.72 1.12455
    swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Rooted 64.5685 69.6269 1.07834
    649 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Ranked 233.725 220.751 1.05877
    grancalcin. [swissprot;acc:p28676] Rooted 64.5659 69.624 1.07834
    retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Squared 29173.8 34362.7 1.17786
    splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Measured 5248.07 5901.72 1.12455
    650 chromodomain y-like protein 2. [refseq;acc:nm_152342] Squared 29016.1 34169.2 1.17759
    golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Measured 8362.81 9402.7 1.12435
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Rooted 64.566 69.6241 1.07834
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Ranked 228.986 216.276 1.05877

    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/