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 401 to 450 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    401 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] RPA1 207.908 226.218 1.08807
    402 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] RPA2
    403 phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] PDC
    404 dna repair protein rad52 homolog. [swissprot;acc:p43351] RAD52
    405 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] CLTCL1 207.931 226.209 1.0879
    406 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] no value 265.634 244.304 1.08731
    407 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] MRPS9 239.75 260.544 1.08673
    408 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] CEBPZ 255.112 234.804 1.08649
    409 rna polymerase i associated factor 53. [refseq;acc:nm_022490] POLR1E 241.045 261.874 1.08641
    410 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] no value 233.376 253.539 1.0864
    411 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] GTF2H1
    412 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] UQCRFSL1 240.788 261.416 1.08567
    413 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] POLR1C 240.913 261.45 1.08525
    414 katanin p60 subunit a 1. [refseq;acc:nm_007044] KATNA1 232.431 252.238 1.08522
    415 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] KATNB1 232.382 252.166 1.08514
    416 dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] POLR1B 240.6 261.041 1.08496
    417 set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] SETMAR 233.539 253.197 1.08417
    418 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] CLEC4M
    419 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] FCER2
    420 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] CD209
    421 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 223.202 205.9 1.08403
    422 ras-related protein rab-37. [swissprot;acc:q96ax2] RAB37 240.287 260.193 1.08284
    423 ras-related protein rab-26. [swissprot;acc:q9ulw5] RAB26
    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] POLR2C
    425 max protein. [swissprot;acc:p25912] MAX 227.828 210.561 1.082
    426 dynactin 4. [refseq;acc:nm_032486] DCTN5 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] POLR2E 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] DDX54 253.852 234.808 1.0811
    429 polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] POLR3G 239.709 259.038 1.08064
    430 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] LSM5 227.748 210.888 1.07995
    431 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] TRUB1 236.245 255.113 1.07987
    432 endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] ENDOG 212.547 229.411 1.07934
    433 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] AIFM1
    434 t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] TBX6
    435 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] POLI 221.522 205.286 1.07909
    436 paxillin. [swissprot;acc:p49023] PXN
    437 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] TRIP10 209.921 226.459 1.07878
    438 n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] ARD1A 233.723 216.674 1.07869
    439 40s ribosomal protein s9. [swissprot;acc:p46781] RPS9 238.986 257.784 1.07866
    440 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] NDC80 231.802 249.983 1.07843
    441 grb2-related adaptor protein. [swissprot;acc:q13588] GRAP 223.457 207.222 1.07835
    442 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] ANKS1B 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] NAV2 223.79 207.539
    444 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] NAV1 223.801 207.549
    445 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] NAV3
    446 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] GRB2 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] NEK2
    448 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] MACF1 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] DST 228.463 246.33 1.07821
    450 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 235.94 218.837 1.07815

    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/