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 1532 to 1581 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    383 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Ranked 237.862 217.739 1.09242
    384 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 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] 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] 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] Rooted 50.7723 46.0607 1.10229
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 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] Measured 4533.74 5279.4 1.16447
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked 266.421 244.236 1.09083
    386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
    60s ribosomal protein l8. [swissprot;acc:p25120] Measured 4533.74 5279.4 1.16447
    protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Rooted 50.0513 45.4124 1.10215
    scratch; scratch 1. [refseq;acc:nm_031309] 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] Squared 15053 18568 1.23351
    hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] 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] Squared 40315.7 49716.4 1.23318
    pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Measured 4533.74 5279.4 1.16447
    serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Rooted 50.3345 45.6718 1.10209
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Ranked 227.575 208.756 1.09015
    389 60s ribosomal protein l34. [swissprot;acc:p49207] Rooted 50.3345 45.6718 1.10209
    arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Squared 31819.7 39222.2 1.23264
    probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Measured 4533.74 5279.4 1.16447
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Ranked 227.575 208.756 1.09015
    390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared 28895.6 35572.8 1.23108
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Rooted 50.3345 45.6718 1.10209
    rw1 protein (fragment). [swissprot;acc:q92545] Measured 4533.74 5279.4 1.16447
    391 40s ribosomal protein s16. [swissprot;acc:p17008] Ranked 241.828 263.62 1.09011
    importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Squared 28895.6 35572.8 1.23108
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Rooted 50.3345 45.6718 1.10209
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Measured 3658.76 3144.39 1.16358
    392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Ranked 241.83 263.615 1.09008
    60s ribosomal protein l3-like. [swissprot;acc:q92901] 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] Measured 3641.89 4236.95 1.16339
    transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Squared 28895.6 35572.8 1.23108
    393 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 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] 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] Ranked 225.719 207.072 1.09005
    transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Squared 28895.6 35572.8 1.23108
    394 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Measured 4490.28 5222.25 1.16301
    dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Ranked 218.827 238.407 1.08948
    mad protein (max dimerizer). [swissprot;acc:q05195] Squared 17248.4 21214 1.22991
    pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Rooted 58.6533 64.5958 1.10132
    395 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Ranked 218.827 238.407 1.08948
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Squared 17254.4 21218.1 1.22972
    protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Rooted 50.0423 45.4523 1.10098
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Measured 4532.73 5269.33 1.16251
    396 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Rooted 116.797 106.111 1.10071

    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/