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 2958 to 3007 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    370 METAP2 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Rooted High confidence 49.7435 45.0586 1.10397
    NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Ranked 242.159 265.104 1.09475
    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 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Low confidence 8551.15 9014.39 1.05417
    AFF2 fragile x mental retardation 2 protein (protein fmr-2) (fmr2p) (ox19 protein) (fragile x e mental retardation syndrome protein). [swissprot;acc:p51816] Ranked 219.599 211.723 1.0372
    CTTN src substrate cortactin (amplaxin) (oncogene ems1). [swissprot;acc:q14247] Squared 49955.6 46676.5 1.07025
    EPB41L1 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] High confidence 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
    SNORD23 glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Rooted Low confidence 70.0201 73.4927 1.04959
    ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] High confidence 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
    AFF3 laf-4 protein (lymphoid nuclear protein related to af4). [swissprot;acc:p51826] Low confidence 219.598 211.722 1.0372
    AUH au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698] Measured 7799.23 8221.54 1.05415
    EPB41L3 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Squared High confidence 45986.7 56776.8 1.23464
    FUCA1 tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Rooted Low confidence 73.2173 76.8476 1.04958
    HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Measured High confidence 5067 5926.17 1.16956
    PUM2 pumilio homolog 2. [refseq;acc:nm_015317] Squared Low confidence 50252.8 46955.6 1.07022
    SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Rooted High confidence 49.3451 54.4606 1.10367
    373 no value guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
    secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Measured Low confidence 7633.63 8043.87 1.05374
    AFF4 all1 fused gene from 5q31. [refseq;acc:nm_014423] Ranked 219.598 211.722 1.0372
    EPB41L2 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Squared High confidence 45986 56776.1 1.23464
    FUCA2 fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] Rooted Low confidence 73.1985 76.827 1.04957
    HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Measured High confidence 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
    PUM1 pumilio homolog 1. [refseq;acc:nm_014676] Squared Low confidence 50239.1 46947.9 1.0701
    374 HS6ST2 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 47709.2 44584.4 1.07009
    HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Measured High confidence 5066.93 5925.38 1.16942
    PFDN1 prefoldin subunit 1. [swissprot;acc:o60925] Low confidence 7633.63 8043.87 1.05374
    PGBD3 excision repair protein ercc-6 (cockayne syndrome protein csb). [swissprot;acc:q03468] Ranked 210.34 202.797 1.03719
    PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Rooted 71.4248 74.9614 1.04952
    RPL26 60s ribosomal protein l26. [swissprot;acc:q02877] High confidence 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 HRBL hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Squared Low confidence 48790.5 45597.6 1.07002
    LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Measured High confidence 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
    SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Low confidence 72.0758 75.639 1.04944
    SDF4 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Squared High confidence 45987 56777.1 1.23463
    SMOC2 secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Measured Low confidence 7633.63 8043.87 1.05374
    SPSB1 spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] Ranked 219.556 211.692 1.03715
    376 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Rooted High confidence 50.2554 45.5688 1.10285
    C10orf83 44050 protein. [refseq;acc:nm_178832] Measured 17385.9 14889.2 1.16769
    CCRN4L nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] Ranked Low confidence 209.328 201.83 1.03715
    CHDH choline dehydrogenase. [refseq;acc:nm_018397] Measured 7633.63 8043.87 1.05374
    DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Ranked High confidence 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
    OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Rooted Low confidence 68.9309 72.3172 1.04913

    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/