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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2558 to 2607 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    640 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] GSTT2B Measured 4811.02 5414.64 1.12547
    intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] no value Ranked 217.67 230.596 1.05938
    nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] QPRT Squared 22848.5 26941.5 1.17914
    641 peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] PAOX Measured 4810.85 5414.21 1.12542
    pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] PRAM1 Ranked 217.67 230.596 1.05938
    synapsin i (brain protein 4.1). [swissprot;acc:p17600] SYN1 Rooted 60.0129 64.7371 1.07872
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] no value 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] PFKL 16123.9 19009.7 1.17898
    atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] ATPIF1 Measured 4810.85 5414.23 1.12542
    intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] no value Ranked 217.67 230.596 1.05938
    ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] SORBS1 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] PFKM Squared 16126.5 19012.6 1.17897
    autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] ATG12 Rooted 87.4586 81.0798 1.07867
    hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] HRBL 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] SMOX 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] PFKP Squared 16156.3 19046 1.17886
    cgthba protein (-14 gene protein). [swissprot;acc:q12980] C16orf35 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] HCCS Measured 4810.85 5414.22 1.12542
    rna polymerase i associated factor 53. [refseq;acc:nm_022490] POLR1E 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] GSTT1 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] HTATSF1 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] no value Squared 22722.5 26786.5 1.17885
    preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] MOBKL3 Rooted 63.1463 68.1044 1.07852
    646 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] no value 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] DNAJB11 Rooted 63.1463 68.1044 1.07852
    fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] FBL Measured 4019.88 4522.61 1.12506
    short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] SCOC Ranked 216.731 229.549 1.05914
    647 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] CAPNS1 Rooted 64.5657 69.6237 1.07834
    cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] CTSB Squared 33384.2 39324.9 1.17795
    dynein light chain 2. [refseq;acc:nm_080677] DYNLL2 Ranked 216.731 229.549 1.05914
    short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] TRPC4 Measured 5167.88 4594.43 1.12481
    648 methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] MARS Ranked 218.227 206.078 1.05895
    retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] RBL1 Squared 29174 34363.5 1.17788
    splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] SF3A3 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] ARID1A 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] EIF4E Ranked 233.725 220.751 1.05877
    grancalcin. [swissprot;acc:p28676] GCA Rooted 64.5659 69.624 1.07834
    retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] RBL2 Squared 29173.8 34362.7 1.17786
    splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] SF3A1 Measured 5248.07 5901.72 1.12455
    650 chromodomain y-like protein 2. [refseq;acc:nm_152342] CDYL2 Squared 29016.1 34169.2 1.17759
    golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] GORASP2 Measured 8362.81 9402.7 1.12435
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] SRI Rooted 64.566 69.6241 1.07834
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] no value Ranked 228.986 216.276 1.05877
    651 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] BAIAP3 233.725 220.751
    ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] TBC1D10A Measured 5168.43 4597.44 1.1242
    programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] PDCD6 Rooted 64.5685 69.6269 1.07834
    testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] CDY1B Squared 29012.2 34163.9 1.17757
    652 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] ARID1B Rooted 64.5672 69.6254 1.07834
    chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] CDYL Squared 29012.2 34163.9 1.17757
    short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] TRPC5 Measured 5168.43 4597.44 1.1242

    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/