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 [...,...].
    Gene Rank description Hugo 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
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    105 vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] VPS33B Rooted Divided Low confidence 69.4249 75.2464 1.08385
    106 atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] ATP5O Squared 61860.4 53172.3 1.1634
    cytohesin 4. [swissprot;acc:q9uia0] PSCD4 High confidence 407289 263351 1.54656
    disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] DLGAP3 Ranked Subtracted Low confidence 197.731 212.069 14.338
    junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 Rooted Divided 57.5193 53.0965 1.0833
    nostrin. [refseq;acc:nm_052946] NOSTRIN Ranked Subtracted High confidence 209.299 249.187 39.888
    nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 Measured Divided 4241.57 5810.79 1.36996
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB Rooted 60.8692 77.7165 1.27678
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A Measured Subtracted 11068 8508.5 2559.5
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 Rooted Low confidence 68.5805 74.7056 6.1251
    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] SEPT4 Squared High confidence 82624.3 115061 32436.7
    solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] SLC16A10 Measured Low confidence 10553.7 11452.6 898.9
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 Ranked Divided 220.497 205.364 1.07369
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] PPP1R2P9 Squared Subtracted 62040.9 53402.5 8638.4
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 Ranked Divided High confidence 252.329 202.004 1.24913
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Rooted Subtracted 63.7477 48.1589 15.5888
    vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] VPS18 Measured Divided Low confidence 7337.57 8055.84 1.09789
    107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 High confidence 4266.04 5843.51 1.36977
    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] CYP27B1 Subtracted Low confidence 3032.56 3915.4 882.84
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 Squared Divided High confidence 407289 263351 1.54656
    eap30 subunit of ell complex. [refseq;acc:nm_007241] SNF8 Ranked Subtracted 209.299 249.187 39.888
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 Rooted Divided 60.875 77.7152 1.27664
    homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 Ranked 252.309 201.998 1.24907
    junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Rooted Low confidence 57.5193 53.0965 1.0833
    methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] MTHFR Squared Subtracted 63248.6 71782.7 8534.1
    mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] FAM89B Ranked Divided 227.429 211.97 1.07293
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] RGL1 Squared Subtracted High confidence 84857.8 53402.4 31455.4
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 Measured 14229.2 16780.7 2551.5
    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] PPP2R2B Rooted 63.7477 48.1594 15.5883
    star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] STARD7 Low confidence 61.8872 67.9229 6.0357
    tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] TP53I3 Measured Divided 11371 12479.2 1.09746
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] PPP1R2P9 Squared 62040.9 53402.5 1.16176
    vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] PTPRA Ranked Subtracted 203.948 189.652 14.296
    108 chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] CXorf9 Squared 55143.2 46609.7 8533.5
    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] CYP27A1 Measured 3035.43 3917.88 882.45
    disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] no value Ranked 197.752 212.031 14.279
    disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] DLGAP3 Divided 197.731 212.069 1.07251
    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] FLNB Measured High confidence 4366.44 5899.76 1.35116
    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] AGL Squared Low confidence 61349.6 52848.4 1.16086
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 Ranked High confidence 252.296 201.995 1.24902
    liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] SLC39A6 Subtracted 209.299 249.187 39.888
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value Squared Divided 19321 12542.6 1.54043
    ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] RALGDS Measured Subtracted 14021.4 11523 2498.4
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 Divided Low confidence 10499 11515.8 1.09685
    Squared Subtracted High confidence 78383 108483 30100
    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] PPP2R2C Rooted 63.7475 48.1615 15.586
    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] SMPD2 Divided Low confidence 57.5193 53.0965 1.0833
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] no value Subtracted 62.4962 68.5193 6.0231
    voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] CACNG2 Divided High confidence 49.2925 62.397 1.26585
    109 44050 protein. [refseq;acc:nm_178832] C10orf83 Measured Subtracted 17385.9 14889.2 2496.7

    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/