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 408 to 457 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		network_comparison
    		green
    408 CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 1.08649 234.804
    409 POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] 241.045 1.08641 261.874
    410 no value tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 233.376 1.0864 253.539
    411 GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]
    412 UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 240.788 1.08567 261.416
    413 POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 1.08525 261.45
    414 KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] 232.431 1.08522 252.238
    415 KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 232.382 1.08514 252.166
    416 POLR1B dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 240.6 1.08496 261.041
    417 SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 233.539 1.08417 253.197
    418 CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]
    419 FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
    420 CD209 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]
    421 TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 223.202 1.08403 205.9
    422 RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] 240.287 1.08284 260.193
    423 RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5]
    424 POLR2C 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 max protein. [swissprot;acc:p25912] 227.828 1.082 210.561
    426 DCTN5 dynactin 4. [refseq;acc:nm_032486] 233.142 1.08197 252.253
    427 POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 239.977 1.08146 259.525
    428 DDX54 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 1.0811 234.808
    429 POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 239.709 1.08064 259.038
    430 LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 227.748 1.07995 210.888
    431 TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 236.245 1.07987 255.113
    432 ENDOG endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 1.07934 229.411
    433 AIFM1 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]
    434 TBX6 t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]
    435 POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 221.522 1.07909 205.286
    436 PXN paxillin. [swissprot;acc:p49023]
    437 TRIP10 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 209.921 1.07878 226.459
    438 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 233.723 1.07869 216.674
    439 RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] 238.986 1.07866 257.784
    440 NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 231.802 1.07843 249.983
    441 GRAP grb2-related adaptor protein. [swissprot;acc:q13588] 223.457 1.07835 207.222
    442 ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 1.0783 207.55
    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] 223.79 207.539
    444 NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 223.801 207.549
    445 NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]
    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
    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]
    448 MACF1 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 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
    450 SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.94 1.07815 218.837
    451 POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 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
    453 SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
    454 no value 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 1.07779 226.578
    455 TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 210.225
    456 ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
    457 UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]

    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/