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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 875 to 924 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		network_comparison
    		green
    438 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Divided 233.723 1.07869 216.674
    BOP1 block of proliferation 1. [swissprot;acc:q14137] Subtracted 250.794 16.361 234.433
    439 PES1 pescadillo homolog 1. [swissprot;acc:o00541] 251.297 16.356 234.941
    RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] Divided 238.986 1.07866 257.784
    440 no value 40s ribosomal protein s26. [swissprot;acc:p02383] Subtracted 210.224 16.354 226.578
    NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Divided 231.802 1.07843 249.983
    441 GRAP grb2-related adaptor protein. [swissprot;acc:q13588] 223.457 1.07835 207.222
    TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Subtracted 210.225 16.353 226.578
    442 ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Divided 223.802 1.0783 207.55
    ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Subtracted 210.225 16.353 226.578
    443 NAV2 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] Divided 223.79 1.0783 207.539
    UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Subtracted 210.225 16.353 226.578
    444 NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Divided 223.801 1.0783 207.549
    NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Subtracted 250.053 16.328 233.725
    445 GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 250.858 16.295 234.563
    NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Divided 223.801 1.0783 207.549
    446 GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 224.049 1.07827 207.785
    Subtracted 16.264
    447 NEK2 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] Divided 1.07827
    Subtracted 16.264
    448 ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 16.252 207.55
    MACF1 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Divided 228.468 1.07822 246.338
    449 DST 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 1.07821 246.33
    NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Subtracted 223.801 16.252 207.549
    450 NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 235.94 1.07815 218.837
    451 NAV2 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] Subtracted 223.79 16.251 207.539
    POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Divided 239.092 1.07785 257.705
    452 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 1.07784 207.972
    POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Subtracted 221.522 16.236 205.286
    453 PXN paxillin. [swissprot;acc:p49023]
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Divided 224.161 1.07784 207.972
    454 no value 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 1.07779 226.578
    GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Subtracted 223.457 16.235 207.222
    455 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 16.189 207.972
    TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided 210.225 1.07779 226.578
    456 ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Subtracted 224.161 16.189 207.972
    457 FNBP1 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 210.578 16.186 226.764
    UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Divided 210.225 1.07779 226.578
    458 DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Subtracted 251.653 16.147 235.506
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 235.922 1.07764 218.925
    459 BAG3 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 1.07748 216.737
    RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Subtracted 250.538 16.137 234.401
    460 RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 186.52 16.1 170.42
    SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Divided 223.648 1.0772 207.62
    461 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Subtracted 186.52 16.1 170.42
    KLF5 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] Divided 223.648 1.0772 207.62
    462 MKI67IP 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 1.07709 236.224
    POLR2H dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Subtracted 236.662 16.046 252.708

    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/