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 1480 to 1529 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    370 SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Measured 4108.15 4808.93 1.17058
    371 EPB41L1 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] Squared 45985.9 56776 1.23464
    HTRA2 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Measured 5067.02 5926.46 1.16961
    RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Ranked 186.52 170.42 1.09447
    ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] Rooted 49.3451 54.4606 1.10367
    372 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Ranked 186.52 170.42 1.09447
    EPB41L3 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Squared 45986.7 56776.8 1.23464
    HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Measured 5067 5926.17 1.16956
    SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Rooted 49.3451 54.4606 1.10367
    373 no value guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
    EPB41L2 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Squared 45986 56776.1 1.23464
    HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Measured 5066.99 5926.1 1.16955
    MRPL11 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Ranked 242.37 265.255 1.09442
    374 HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Measured 5066.93 5925.38 1.16942
    RPL26 60s ribosomal protein l26. [swissprot;acc:q02877] Rooted 50.2549 45.5599 1.10305
    SPTBN5 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Squared 45987 56777.1 1.23463
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked 267.208 244.168 1.09436
    375 LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Measured 4700.42 5492.63 1.16854
    POLR3A dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Ranked 242.686 265.516 1.09407
    RPL35 60s ribosomal protein l35. [swissprot;acc:p42766] Rooted 50.2545 45.5637 1.10295
    SDF4 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Squared 45987 56777.1 1.23463
    376 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Rooted 50.2554 45.5688 1.10285
    C10orf83 44050 protein. [refseq;acc:nm_178832] Measured 17385.9 14889.2 1.16769
    DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Ranked 257.017 234.945 1.09395
    LGALS4 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared 46021.4 56813.2 1.2345
    377 MRPL2 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Rooted 50.2554 45.5687 1.10285
    ODC1 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Squared 33044.9 40781.4 1.23412
    POLR1A dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked 242.691 265.481 1.09391
    PPP1R8 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] Measured 17385.9 14889.2 1.16769
    378 EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared 15034.5 18552.2 1.23398
    MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Rooted 50.5816 45.8738 1.10263
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured 12471.7 14561.7 1.16758
    RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked 242.593 265.365 1.09387
    379 AASS aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Squared 33010.8 40732.2 1.23391
    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

    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/