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 1680 to 1729 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    105 VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Rooted Divided Low confidence 69.4249 75.2464 1.08385
    106 ATP5O atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Squared 61860.4 53172.3 1.1634
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Measured Subtracted High confidence 11068 8508.5 2559.5
    COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Ranked Divided 252.329 202.004 1.24913
    DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Subtracted Low confidence 197.731 212.069 14.338
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted 68.5805 74.7056 6.1251
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked Divided 220.497 205.364 1.07369
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted High confidence 60.8692 77.7165 1.27678
    JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Low confidence 57.5193 53.0965 1.0833
    NOSTRIN nostrin. [refseq;acc:nm_052946] Ranked Subtracted High confidence 209.299 249.187 39.888
    PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared Low confidence 62040.9 53402.5 8638.4
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted High confidence 63.7477 48.1589 15.5888
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Squared Divided 407289 263351 1.54656
    SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Subtracted 82624.3 115061 32436.7
    SLC16A10 solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] Measured Low confidence 10553.7 11452.6 898.9
    VPS18 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Divided 7337.57 8055.84 1.09789
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] High confidence 4241.57 5810.79 1.36996
    107 CYP27B1 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Subtracted Low confidence 3032.56 3915.4 882.84
    FAM89B mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] Ranked Divided 227.429 211.97 1.07293
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted High confidence 60.875 77.7152 1.27664
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 201.998 1.24907
    JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Rooted Low confidence 57.5193 53.0965 1.0833
    MTHFR methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Squared Subtracted 63248.6 71782.7 8534.1
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Measured Divided High confidence 4266.04 5843.51 1.36977
    PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared Low confidence 62040.9 53402.5 1.16176
    PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Rooted Subtracted High confidence 63.7477 48.1594 15.5883
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Squared Divided 407289 263351 1.54656
    PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Ranked Subtracted Low confidence 203.948 189.652 14.296
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared High confidence 84857.8 53402.4 31455.4
    SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured 14229.2 16780.7 2551.5
    SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] Ranked 209.299 249.187 39.888
    STARD7 star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Rooted Low confidence 61.8872 67.9229 6.0357
    TP53I3 tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Measured Divided 11371 12479.2 1.09746
    108 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Ranked Subtracted 197.752 212.031 14.279
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared Divided High confidence 19321 12542.6 1.54043
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Rooted Subtracted Low confidence 62.4962 68.5193 6.0231
    AGL glycogen debranching enzyme (glycogen debrancher) [includes: 4-alpha- glucanotransferase (ec 2.4.1.25) (oligo-1,4-1,4-glucantransferase); amylo-alpha-1,6-glucosidase (ec 3.2.1.33) (amylo-1,6-glucosidase) (dextrin 6-alpha-d-glucosidase)]. [swissprot;acc:p35573] Squared Divided 61349.6 52848.4 1.16086
    CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Rooted High confidence 49.2925 62.397 1.26585
    CXorf9 chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] Squared Subtracted Low confidence 55143.2 46609.7 8533.5
    CYP27A1 cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] Measured 3035.43 3917.88 882.45
    DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Ranked Divided 197.731 212.069 1.07251
    FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Measured High confidence 4366.44 5899.76 1.35116
    HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked 252.296 201.995 1.24902
    PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Rooted Subtracted 63.7475 48.1615 15.586
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 14021.4 11523 2498.4
    SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Divided Low confidence 10499 11515.8 1.09685
    Squared Subtracted High confidence 78383 108483 30100
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Ranked 209.299 249.187 39.888
    SMPD2 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Rooted Divided Low confidence 57.5193 53.0965 1.0833
    109 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared Subtracted High confidence 88432.6 58423.3 30009.3

    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/