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 Network Comparison Type Gene Hugo Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1508 to 1557 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    377 PPP1R8 Measured nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] 17385.9 14889.2 1.16769
    378 EIF4G3 Squared eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 15034.5 18552.2 1.23398
    MRPL4 Rooted mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 50.5816 45.8738 1.10263
    NFU1 Measured hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 12471.7 14561.7 1.16758
    RPL30 Ranked 60s ribosomal protein l30. [swissprot;acc:p04645] 242.593 265.365 1.09387
    379 AASS Squared aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 33010.8 40732.2 1.23391
    AK2 Ranked adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 241.509 264.163 1.0938
    GULP1 Rooted ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] 59.5128 65.604 1.10235
    RRM2 Measured ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 6704.44 7811.45 1.16512
    380 no value Ranked suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 242.109 264.79 1.09368
    ACADVL Measured acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 12998.5 15138.2 1.16461
    ADC Squared ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] 32991.5 40704.5 1.23379
    CAPS Rooted calcyphosine. [swissprot;acc:q13938] 59.5128 65.604 1.10235
    381 AZIN1 Squared ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] 32987.4 40698.5 1.23376
    CRNKL1 Rooted crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 59.5128 65.604 1.10235
    SCYE1 Measured multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 5246.01 6109.31 1.16456
    TAF7 Ranked transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 200.586 183.423 1.09357
    382 no value Squared rna-binding protein. [refseq;acc:nm_019027] 15043.7 18560.1 1.23375
    PARK2 Measured parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 4533.74 5279.4 1.16447
    RPS23 Rooted 40s ribosomal protein s23. [swissprot;acc:p39028] 49.8325 45.2077 1.1023
    TAF7L Ranked 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] 200.791 183.66 1.09328
    383 no value Measured hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] 4533.74 5279.4 1.16447
    Squared apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 15043.7 18560.1 1.23375
    MRPS12 Rooted 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 49.8325 45.2077 1.1023
    RBM39 Ranked rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 217.739 1.09242
    384 no value Measured cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 4533.74 5279.4 1.16447
    Rooted 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 50.7723 46.0607 1.10229
    E2F1 Ranked 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] 266.421 244.236 1.09083
    SYNCRIP Squared ns1-associated protein 1. [refseq;acc:nm_006372] 15043.7 18560.1 1.23375
    385 BCCIP Rooted 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] 50.7723 46.0607 1.10229
    E2F2 Ranked transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 266.421 244.236 1.09083
    HNRNPR Squared heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 15043.7 18560.1 1.23375
    PSIP1 Measured pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 4533.74 5279.4 1.16447
    386 no value Squared scratch; scratch 1. [refseq;acc:nm_031309] 40388.9 49827.5 1.23369
    EIF1B Rooted protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 50.0513 45.4124 1.10215
    RPL8 Measured 60s ribosomal protein l8. [swissprot;acc:p25120] 4533.74 5279.4 1.16447
    RPS14 Ranked 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
    387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
    Rooted 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 50.3345 45.6718 1.10209
    EIF4G1 Squared eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 15053 18568 1.23351
    HDGF Measured hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] 4533.74 5279.4 1.16447
    388 no value Ranked small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 227.575 208.756 1.09015
    Squared dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 40315.7 49716.4 1.23318
    HDGFL1 Measured pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] 4533.74 5279.4 1.16447
    SRR Rooted serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 50.3345 45.6718 1.10209
    389 DDX6 Measured probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 4533.74 5279.4 1.16447
    RARS2 Squared arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 31819.7 39222.2 1.23264
    RPL34 Rooted 60s ribosomal protein l34. [swissprot;acc:p49207] 50.3345 45.6718 1.10209
    SNRPF Ranked small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 227.575 208.756 1.09015
    390 no value Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 28895.6 35572.8 1.23108

    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/