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 red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1762 to 1811 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    221 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] HPRT1 Squared High confidence 70739 93908.8 1.32754
    myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] no value Ranked 112 126 1.125
    serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] MAK Rooted Low confidence 84.7778 89.7815 1.05902
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A High confidence 56.9506 64.7888 1.13763
    tata element modulatory factor (tmf). [swissprot;acc:p82094] TMF1 Squared Low confidence 54650.6 49501.5 1.10402
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] BACH2 Ranked 172.647 164.44 1.04991
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value Measured 10491.4 9831.19 1.06715
    222 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] RBBP4 Rooted High confidence 52.7936 60.0592 1.13762
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 Measured 41482.5 33356.5 1.24361
    dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] MYH7B Ranked 112 126 1.125
    homeobox protein engrailed-1 (hu-en-1). [swissprot;acc:q05925] EN1 Squared Low confidence 51065.6 46267.8 1.1037
    intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] ICK Rooted 84.7145 89.7052 1.05891
    phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] PSAT1 Measured 9556.43 10196.2 1.06695
    signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] STAM2 Squared High confidence 86281 65058.3 1.32621
    ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] UBE2E1 Ranked Low confidence 203.935 214.089 1.04979
    223 cytohesin 4. [swissprot;acc:q9uia0] PSCD4 Measured High confidence 41482.5 33356.5 1.24361
    general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [refseq;acc:nm_012086] GTF3C3 Ranked Low confidence 217.228 206.926 1.04979
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 Rooted High confidence 137.446 120.823 1.13758
    microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] no value Low confidence 71.4919 75.687 1.05868
    myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] MYH13 Ranked High confidence 112 126 1.125
    snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966] SNAPC3 Squared Low confidence 51606.9 46815.7 1.10234
    t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] TCP1 High confidence 40982.6 54272.3 1.32428
    tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] TPM3 Measured Low confidence 7600.32 8107.39 1.06672
    224 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 High confidence 41482.5 33356.5 1.24361
    hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 Rooted 137.446 120.823 1.13758
    large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] SLC7A8 Low confidence 67.8657 71.8432 1.05861
    malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] LENG4 Measured 6228.87 5839.8 1.06662
    microfibrillar-associated protein 1. [swissprot;acc:p55081] MFAP1 Squared 51606.9 46815.7 1.10234
    oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] SLC15A2 Ranked High confidence 185.969 165.623 1.12285
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Squared 14943.9 19771.9 1.32307
    ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] UBE2E4P Ranked Low confidence 203.933 214.059 1.04965
    225 40s ribosomal protein s8. [swissprot;acc:p09058] RPS8 Squared 52226.7 47386.3 1.10215
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value Rooted High confidence 137.446 120.823 1.13758
    metaxin 1. [swissprot;acc:q13505] MTX1 Squared 60401.6 79875.7 1.32241
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value Measured 9035 7279.6 1.24114
    oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 Ranked Low confidence 201.41 191.974 1.04915
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF Rooted 70.9202 75.0544 1.05829
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 Ranked High confidence 226.471 201.769 1.12243
    tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] TPM1 Measured Low confidence 7604 8109.6 1.06649
    226 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] ANKRD7 Rooted 66.7906 70.6819 1.05826
    cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP Ranked High confidence 239.991 269.238 1.12187
    lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] LEF1 Low confidence 208.289 198.538 1.04911
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 Rooted High confidence 137.446 120.823 1.13758
    myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 Measured 9035 7279.6 1.24114
    ninein (gsk3b interacting protein). [refseq;acc:nm_016350] NIN Low confidence 7393.41 7880.73 1.06591
    oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] SLC15A2 Squared High confidence 73510.2 55607.3 1.32195
    peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] PIN1 Low confidence 52729.7 47863.5 1.10167
    227 breast cancer antigen ny-br-1. [refseq;acc:nm_052997] ANKRD30A Rooted 66.7948 70.6853 1.05825
    bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] BRD4 Squared 53295.8 48379.3 1.10162
    c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] TENC1 Ranked 216.404 206.277 1.04909

    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/