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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1558 to 1607 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    98 GTF3A transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Divided Measured Low confidence 7624.8 1.1006 8391.85
    KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Squared High confidence 227160 1.55505 146079
    LBX1 transcription factor lbx1. [swissprot;acc:p52954] Rooted 47.6504 1.29028 36.9304
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked 88.2482 1.24949 110.265
    MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Subtracted Rooted Low confidence 63.1259 6.3046 69.4305
    PHF12 phd finger protein 12; phd zinc finger transcription factor. [refseq;acc:nm_020889] Divided Squared 61253.4 1.17845 51977.8
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted Measured 12376.5 940 11436.5
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided High confidence 2353.63 1.3705 3225.65
    SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Subtracted Squared 89578.7 36304.3 125883
    SLC7A6 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Divided Ranked Low confidence 200.497 1.0798 185.679
    Subtracted 14.818
    99 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Divided Measured 5752.65 1.10037 6330.03
    jun dimerization protein. [refseq;acc:nm_130469] Subtracted Ranked High confidence 204.641 43.684 160.957
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Measured Low confidence 12376.4 939.9 11436.5
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided Ranked High confidence 88.2482 1.24949 110.265
    BRP44 brain protein 44. [swissprot;acc:o95563] Subtracted Squared 89182.8 36046.2 125229
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided Rooted Low confidence 68.5805 1.08931 74.7056
    EIF4B eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Ranked 200.497 1.0798 185.679
    Subtracted 14.818
    GPSM2 mosaic protein lgn. [swissprot;acc:p81274] Divided Rooted High confidence 47.6504 1.29028 36.9304
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted Low confidence 96.9641 6.2779 103.242
    RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Divided Squared 61163.4 1.17794 51924
    SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 59884.7 8966.1 68850.8
    SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Measured High confidence 15999.1 3008 19007.1
    SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Divided 2353.63 1.3705 3225.65
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Subtracted Rooted 19.9625 15.8355 35.798
    WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Divided Squared 226186 1.55382 145568
    100 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
    FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Measured 2353.63 1.3705 3225.65
    FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Subtracted Ranked 204.641 43.595 161.046
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 88.2482 1.24949 110.265
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted Measured Low confidence 12375.5 939.7 11435.8
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Divided Rooted High confidence 47.6504 1.29028 36.9304
    SEPT6 septin 6. [swissprot;acc:q14141] Subtracted Measured 15959.9 2997.2 18957.1
    SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 89182.8 36046.2 125229
    SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Divided Rooted Low confidence 63.7749 1.08901 69.4515
    SLC16A2 monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] Subtracted Squared 63904 8887.6 72791.6
    SLC7A9 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Divided Ranked 200.497 1.0798 185.679
    Subtracted 14.818
    SMYD2 set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Divided Measured 5752.65 1.10037 6330.03
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted Rooted 61.9982 6.2355 68.2337
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 19.9625 15.8355 35.798
    TP53I3 tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Divided Squared Low confidence 70019.5 1.17533 82296.2
    101 no value raptor; p150 target of rapamycin (tor)-scaffold protein containing wd-repeats. [refseq;acc:nm_020761] 63526.9 1.16811 54384.3
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] High confidence 222655 1.5507 143584
    CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 1.3705 3225.65
    DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Subtracted Rooted 19.9625 15.8355 35.798
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence 68.4921 6.1956 74.6877
    F13A1 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Ranked 226.395 14.682 211.713
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence 204.641 43.59 161.051

    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/