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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2630 to 2679 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    658 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] no value Ranked 229.072 216.576 1.0577
    eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] EIF3B Rooted 52.7523 56.8686 1.07803
    similar to trna synthetase class ii. [refseq;acc:nm_152268] PARS2 Squared 22293.8 26242.6 1.17713
    659 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] MRPS9 Rooted 51.7081 47.9816 1.07767
    hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] HEY1 Ranked 229.072 216.576 1.0577
    ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] OTC Squared 24614 28973.4 1.17711
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] SHROOM3 Measured 6089.21 6835.34 1.12253
    660 actin binding lim protein 2. [refseq;acc:nm_032432] ABLIM2 Ranked 229.072 216.576 1.0577
    fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 Rooted 133.216 123.627 1.07756
    nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] NDUFB9 Squared 33024.9 38867.8 1.17692
    u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] no value Measured 5575.18 6254.85 1.12191
    661 delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] ALAD Squared 22223.1 26152.4 1.17681
    hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] HEYL Ranked 229.072 216.576 1.0577
    nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] NXF5 Rooted 68.8243 74.1496 1.07738
    step ii splicing factor slu7. [refseq;acc:nm_006425] SLU7 Measured 5575.18 6254.85 1.12191
    662 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] NXF3 Rooted 68.8237 74.1484 1.07737
    partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] PARD6G Measured 6374.65 7145.59 1.12094
    synapsin ii. [swissprot;acc:q92777] SYN2 Ranked 229.072 216.576 1.0577
    ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] no value Squared 23947.4 28163.7 1.17607
    663 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] ACRC 23947.7 28163.9 1.17606
    mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] MRRF Ranked 229.072 216.576 1.0577
    nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] NXF1 Rooted 68.8197 74.1413 1.07733
    tubby protein homolog. [swissprot;acc:p50607] TUB Measured 6374.65 7145.59 1.12094
    664 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] NET1 Rooted 51.6042 55.574 1.07693
    peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] PEX5 Ranked 229.072 216.576 1.0577
    protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] PRKCI Measured 6374.65 7145.59 1.12094
    ubiquitin-like protein smt3a. [swissprot;acc:p55854] SUMO3 Squared 23948 28164.1 1.17605
    665 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] HEY2 Ranked 229.072 216.576 1.0577
    numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] NUMB Measured 6374.65 7145.59 1.12094
    rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] ARHGEF3 Rooted 51.6042 55.574 1.07693
    u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] LSM6 Squared 18960.3 22298 1.17604
    666 down-regulated in metastasis. [refseq;acc:nm_014503] UTP20 Rooted 51.6042 55.574 1.07693
    glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] SLC37A1 Squared 29224 34362.1 1.17582
    tbc1 domain family member 5. [swissprot;acc:q92609] TBC1D5 Measured 6374.65 7145.59 1.12094
    transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] HES1 Ranked 229.072 216.576 1.0577
    667 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] ECH1
    proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] PRODH Squared 29224 34362.1 1.17582
    tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] TULP1 Measured 6374.65 7145.59 1.12094
    ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] UQCRFSL1 Rooted 51.2483 47.5889 1.0769
    668 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] ABLIM1 Ranked 229.072 216.576 1.0577
    acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL Rooted 95.4476 102.785 1.07687
    isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] no value Squared 23969.3 28175.3 1.17547
    vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] VPS29 Measured 6374.65 7145.59 1.12094
    669 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] HPRT1 Rooted 79.931 86.0693 1.07679
    numb-like protein (numb-r). [swissprot;acc:q9y6r0] NUMBL Measured 6374.65 7145.59 1.12094
    synapsin i (brain protein 4.1). [swissprot;acc:p17600] SYN1 Ranked 229.072 216.576 1.0577
    u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] LSM4 Squared 18548.7 21798.2 1.17519
    670 autoantigen ngp-1. [swissprot;acc:q13823] GNL2 Ranked 250.302 236.817 1.05694
    dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] POLR1C Rooted 51.2122 47.5637 1.07671
    dok-like protein. [refseq;acc:nm_024872] no value Squared 28911 33971.3 1.17503

    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/