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 3858 to 3907 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    965 NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Rooted 52.9804 50.0947 1.0576
    PARD6G partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Ranked 211.987 204.964 1.03426
    PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Measured 11773.7 10733.8 1.09688
    966 FUT8 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Squared 22271.9 25656.8 1.15198
    HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Rooted 52.9804 50.0947 1.0576
    LGALS4 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Measured 7817.9 8575.12 1.09686
    TUB tubby protein homolog. [swissprot;acc:p50607] Ranked 211.987 204.964 1.03426
    967 no value poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Squared 25580.6 29466.1 1.15189
    EPB41 protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Measured 7813.35 8569.96 1.09684
    PRKCI protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Ranked 211.987 204.964 1.03426
    RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Rooted 52.9804 50.0947 1.0576
    968 HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
    MTO1 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Squared 25580.6 29466.1 1.15189
    NUMB numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Ranked 211.987 204.964 1.03426
    SPTBN5 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Measured 7813.48 8570.11 1.09684
    969 EPB41L1 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 7813.34 8569.95
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Squared 19488.7 22447.5 1.15182
    RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] Rooted 52.9804 50.0947 1.0576
    TBC1D5 tbc1 domain family member 5. [swissprot;acc:q92609] Ranked 211.987 204.964 1.03426
    970 EPB41L3 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Measured 7813.45 8570.07 1.09684
    GLUL glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Squared 24426.8 28125 1.1514
    PLEKHF2 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Rooted 61.6649 65.1892 1.05715
    TULP1 tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Ranked 211.987 204.964 1.03426
    971 ACSS2 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] Squared 27478.1 31623.7 1.15087
    EPB41L2 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Measured 7813.36 8569.97 1.09684
    SRD5A1 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Rooted 61.6649 65.1892 1.05715
    VPS29 vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Ranked 211.987 204.964 1.03426
    972 NUMBL numb-like protein (numb-r). [swissprot;acc:q9y6r0]
    SDF4 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Measured 7813.48 8570.11 1.09684
    SRD5A2 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Rooted 61.6649 65.1892 1.05715
    TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Squared 21083.8 24262 1.15074
    973 CDC25C m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Rooted 49.307 52.1123 1.05689
    LGALS9 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Measured 7810.11 8566.29 1.09682
    SLC27A4 solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Squared 27404 31534 1.15071
    TULP3 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Ranked 211.987 204.964 1.03426
    974 FMO2 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Measured 5365.06 5884.52 1.09682
    TM7SF2 delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] Squared 27403.4 31533.3 1.15071
    UBP1 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Rooted 61.8392 65.3085 1.0561
    VPS35 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Ranked 211.987 204.964 1.03426
    975 FMO1 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Measured 5365.14 5884.43 1.09679
    LBR lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Squared 27403.4 31533.3 1.15071
    PRKCZ protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Ranked 211.987 204.964 1.03426
    TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Rooted 61.8392 65.3085 1.0561
    976 FMO4 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Measured 5365.22 5884.32 1.09675
    SLC27A3 solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Squared 27403.7 31533.7 1.15071
    TFCP2L1 lbp-9. [refseq;acc:nm_014553] Rooted 61.8392 65.3085 1.0561
    WDR36 t-cell activation wd repeat protein. [refseq;acc:nm_139281] Ranked 243.34 235.322 1.03407
    977 MPHOSPH10 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Measured 4115.9 4513.14 1.09651
    PFDN5 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Ranked 228.953 221.421 1.03402
    SFRS3 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Rooted 61.8392 65.3085 1.0561

    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/