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 description Gene Hugo Network Comparison Type Value Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1525 to 1574 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    382 40s ribosomal protein s23. [swissprot;acc:p39028] RPS23 Rooted 49.8325 45.2077 1.1023
    parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] PARK2 Measured 4533.74 5279.4 1.16447
    rna-binding protein. [refseq;acc:nm_019027] no value Squared 15043.7 18560.1 1.23375
    tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] TAF7L Ranked 200.791 183.66 1.09328
    383 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] MRPS12 Rooted 49.8325 45.2077 1.1023
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value Squared 15043.7 18560.1 1.23375
    hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Measured 4533.74 5279.4 1.16447
    rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] RBM39 Ranked 237.862 217.739 1.09242
    384 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] no value Rooted 50.7723 46.0607 1.10229
    cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Measured 4533.74 5279.4 1.16447
    ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Squared 15043.7 18560.1 1.23375
    transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] E2F1 Ranked 266.421 244.236 1.09083
    385 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] BCCIP Rooted 50.7723 46.0607 1.10229
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR Squared 15043.7 18560.1 1.23375
    pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] PSIP1 Measured 4533.74 5279.4 1.16447
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 Ranked 266.421 244.236 1.09083
    386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] RPS14 242.238 264.11 1.09029
    60s ribosomal protein l8. [swissprot;acc:p25120] RPL8 Measured 4533.74 5279.4 1.16447
    protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B Rooted 50.0513 45.4124 1.10215
    scratch; scratch 1. [refseq;acc:nm_031309] no value Squared 40388.9 49827.5 1.23369
    387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Ranked 242.238 264.11 1.09029
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Rooted 50.3345 45.6718 1.10209
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Squared 15053 18568 1.23351
    hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] HDGF Measured 4533.74 5279.4 1.16447
    388 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] no value Squared 40315.7 49716.4 1.23318
    pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] HDGFL1 Measured 4533.74 5279.4 1.16447
    serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR Rooted 50.3345 45.6718 1.10209
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] no value Ranked 227.575 208.756 1.09015
    389 60s ribosomal protein l34. [swissprot;acc:p49207] RPL34 Rooted 50.3345 45.6718 1.10209
    arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] RARS2 Squared 31819.7 39222.2 1.23264
    probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] DDX6 Measured 4533.74 5279.4 1.16447
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF Ranked 227.575 208.756 1.09015
    390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] MRPL13 241.828 263.62 1.09011
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] no value Squared 28895.6 35572.8 1.23108
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 Rooted 50.3345 45.6718 1.10209
    rw1 protein (fragment). [swissprot;acc:q92545] TMEM131 Measured 4533.74 5279.4 1.16447
    391 40s ribosomal protein s16. [swissprot;acc:p17008] RPS16 Ranked 241.828 263.62 1.09011
    importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] KPNB1 Squared 28895.6 35572.8 1.23108
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1 Rooted 50.3345 45.6718 1.10209
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP Measured 3658.76 3144.39 1.16358
    392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] RPL13A Ranked 241.83 263.615 1.09008
    60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L Rooted 50.3313 45.6913 1.10155
    atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] DDX54 Measured 3641.89 4236.95 1.16339
    transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] TBL1X Squared 28895.6 35572.8 1.23108
    393 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] POLR2A Rooted 49.8842 45.2875 1.1015
    eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] EIF4E Measured 4490.28 5222.25 1.16301
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A Ranked 225.719 207.072 1.09005
    transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] TBL1Y Squared 28895.6 35572.8 1.23108
    394 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] BAIAP3 Measured 4490.28 5222.25 1.16301
    dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] DPP9 Ranked 218.827 238.407 1.08948

    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/