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 418 to 467 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    description
    red
    green
    network_comparison
    418 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 233.539 253.197 1.08417
    419 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
    420 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]
    421 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 223.202 205.9 1.08403
    422 ras-related protein rab-37. [swissprot;acc:q96ax2] 240.287 260.193 1.08284
    423 ras-related protein rab-26. [swissprot;acc:q9ulw5]
    424 dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
    425 max protein. [swissprot;acc:p25912] 227.828 210.561 1.082
    426 dynactin 4. [refseq;acc:nm_032486] 233.142 252.253 1.08197
    427 dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 239.977 259.525 1.08146
    428 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 253.852 234.808 1.0811
    429 polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 239.709 259.038 1.08064
    430 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 227.748 210.888 1.07995
    431 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 236.245 255.113 1.07987
    432 endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 229.411 1.07934
    433 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]
    434 t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]
    435 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 221.522 205.286 1.07909
    436 paxillin. [swissprot;acc:p49023]
    437 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 209.921 226.459 1.07878
    438 n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 233.723 216.674 1.07869
    439 40s ribosomal protein s9. [swissprot;acc:p46781] 238.986 257.784 1.07866
    440 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 231.802 249.983 1.07843
    441 grb2-related adaptor protein. [swissprot;acc:q13588] 223.457 207.222 1.07835
    442 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 207.55 1.0783
    443 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 223.79 207.539
    444 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 223.801 207.549
    445 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]
    446 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 224.049 207.785 1.07827
    447 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955]
    448 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 228.468 246.338 1.07822
    449 bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 228.463 246.33 1.07821
    450 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.94 218.837 1.07815
    451 polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 239.092 257.705 1.07785
    452 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 207.972 1.07784
    453 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
    454 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
    455 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 210.225
    456 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
    457 ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]
    458 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.922 218.925 1.07764
    459 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] 233.529 216.737 1.07748
    460 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 223.648 207.62 1.0772
    461 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]
    462 mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 254.434 236.224 1.07709
    463 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 238.921 257.327 1.07704
    464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 210.578 226.764 1.07686
    465 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 248.152 267.226
    466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
    467 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]

    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/