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 1777 to 1826 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    445 NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Ranked 223.801 207.549 1.0783
    NOC3L ad24 protein. [refseq;acc:nm_022451] Measured 3753.71 4315.95 1.14978
    RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] Rooted 50.1635 45.7274 1.09701
    UBE2E4P ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Squared 58831 48584.2 1.21091
    446 EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Rooted 54.9019 60.2111 1.0967
    GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Measured 3766.03 4329.37 1.14958
    GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Ranked 224.049 207.785 1.07827
    SORBS1 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Squared 29335.6 35515.5 1.21066
    447 ADI1 sipl protein. [refseq;acc:nm_018269] 30155.1 36495 1.21024
    BAIAP3 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Rooted 54.9019 60.2111 1.0967
    NEK2 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Ranked 224.049 207.785 1.07827
    PES1 pescadillo homolog 1. [swissprot;acc:o00541] Measured 3751.14 4310.89 1.14922
    448 CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Squared 20350.3 16816.1 1.21017
    MACF1 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked 228.468 246.338 1.07822
    SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Rooted 50.1671 45.7563 1.0964
    SORBS1 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Measured 6259.3 7190.91 1.14884
    449 CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Squared 20348.5 16817.2 1.20998
    DST bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Ranked 228.463 246.33 1.07821
    POLR2B dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Rooted 50.162 45.7659 1.09606
    WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Measured 3761.59 4319.69 1.14837
    450 ACACB acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] Squared 31646.1 38288.7 1.2099
    CMPK ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Rooted 50.4595 46.0411 1.09597
    MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Measured 4889.21 5610.52 1.14753
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Ranked 235.94 218.837 1.07815
    451 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Squared 17543.3 21222.5 1.20972
    MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Rooted 50.268 45.8663 1.09597
    MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] Measured 4889.71 5610.69 1.14745
    POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Ranked 239.092 257.705 1.07785
    452 no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted 50.4595 46.0415 1.09596
    ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Ranked 224.161 207.972 1.07784
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Squared 17543.3 21222.5 1.20972
    ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] Measured 3760.8 4315.06 1.14738
    453 MED22 surfeit locus protein 5. [swissprot;acc:q15528] Rooted 50.4595 46.0413 1.09596
    PPP6C serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Squared 31620.5 38250.7 1.20968
    SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Measured 3760.8 4315.06 1.14738
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Ranked 224.161 207.972 1.07784
    454 no value 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
    guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Measured 3760.8 4315.06 1.14738
    AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Rooted 50.4595 46.0412 1.09596
    SAPS3 sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Squared 31620.5 38250.7 1.20968
    455 ACACA acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 31597.8 38216.9 1.20948
    GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Measured 4890.51 5610.95 1.14731
    SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Rooted 50.4595 46.0413 1.09596
    TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Ranked 210.225 226.578 1.07779
    456 no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Measured 4890.51 5610.95 1.14731
    ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Ranked 210.225 226.578 1.07779
    NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Squared 10933.6 13219.6 1.20908
    PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Rooted 50.4595 46.0413 1.09596
    457 NDUFS8 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Measured 4890.51 5610.95 1.14731
    NXF3 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Squared 10936.1 13221.9 1.20901

    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/