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 green network_comparison
    Results: HTML CSV LaTeX Showing element 1514 to 1563 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    379 AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked 241.509 264.163 1.0938
    GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted 59.5128 65.604 1.10235
    RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Measured 6704.44 7811.45 1.16512
    380 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Ranked 242.109 264.79 1.09368
    ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Measured 12998.5 15138.2 1.16461
    ADC ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Squared 32991.5 40704.5 1.23379
    CAPS calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 65.604 1.10235
    381 AZIN1 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Squared 32987.4 40698.5 1.23376
    CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 59.5128 65.604 1.10235
    SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Measured 5246.01 6109.31 1.16456
    TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Ranked 200.586 183.423 1.09357
    382 no value rna-binding protein. [refseq;acc:nm_019027] Squared 15043.7 18560.1 1.23375
    PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Measured 4533.74 5279.4 1.16447
    RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] Rooted 49.8325 45.2077 1.1023
    TAF7L 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] Ranked 200.791 183.66 1.09328
    383 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 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
    MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Rooted 49.8325 45.2077 1.1023
    RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Ranked 237.862 217.739 1.09242
    384 no value 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
    E2F1 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
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Squared 15043.7 18560.1 1.23375
    385 BCCIP 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
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked 266.421 244.236 1.09083
    HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Squared 15043.7 18560.1 1.23375
    PSIP1 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
    386 no value scratch; scratch 1. [refseq;acc:nm_031309] Squared 40388.9 49827.5 1.23369
    EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Rooted 50.0513 45.4124 1.10215
    RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] Measured 4533.74 5279.4 1.16447
    RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Ranked 242.238 264.11 1.09029
    387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Rooted 50.3345 45.6718 1.10209
    EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Squared 15053 18568 1.23351
    HDGF 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 no value 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
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Ranked 227.575 208.756 1.09015
    HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Measured 4533.74 5279.4 1.16447
    SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Rooted 50.3345 45.6718 1.10209
    389 DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Measured 4533.74 5279.4 1.16447
    RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Squared 31819.7 39222.2 1.23264
    RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] Rooted 50.3345 45.6718 1.10209
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Ranked 227.575 208.756 1.09015
    390 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared 28895.6 35572.8 1.23108
    MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Ranked 241.828 263.62 1.09011
    SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Rooted 50.3345 45.6718 1.10209
    TMEM131 rw1 protein (fragment). [swissprot;acc:q92545] Measured 4533.74 5279.4 1.16447
    391 KPNB1 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Squared 28895.6 35572.8 1.23108
    RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] Ranked 241.828 263.62 1.09011
    SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Rooted 50.3345 45.6718 1.10209

    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/