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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 825 to 874 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    104 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP Subtracted Measured 11068 8508.5 2559.5
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 Divided Squared 407289 263351 1.54656
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 Ranked 252.371 202.016 1.24926
    jun dimerization protein. [refseq;acc:nm_130469] no value Rooted 60.8365 77.7233 1.27758
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T Subtracted Squared 121579 87259.3 34319.7
    musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 Divided Measured 4241.57 5810.79 1.36996
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 Subtracted Rooted 19.9625 35.798 15.8355
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP Ranked 256.228 298.438 42.21
    105 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 Divided Squared 407289 263351 1.54656
    fos-related antigen 2. [swissprot;acc:p15408] FOSL2 Rooted 60.8675 77.7168 1.27682
    guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] GNB1 Ranked 266.716 333.165 1.24914
    musashi 1. [refseq;acc:nm_002442] MSI1 Measured 4241.57 5810.79 1.36996
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 Subtracted 11068 8508.5 2559.5
    ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] RALGDS Squared 90432.9 56304.2 34128.7
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] no value Rooted 63.7477 48.1588 15.5889
    transcription factor jun-d. [swissprot;acc:p17535] JUND Ranked 200.941 158.941 42
    106 cytohesin 4. [swissprot;acc:q9uia0] PSCD4 Divided Squared 407289 263351 1.54656
    nostrin. [refseq;acc:nm_052946] NOSTRIN Subtracted Ranked 209.299 249.187 39.888
    nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 Divided Measured 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 Subtracted Measured 11068 8508.5 2559.5
    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 82624.3 115061 32436.7
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 Divided Ranked 252.329 202.004 1.24913
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Subtracted Rooted 63.7477 48.1589 15.5888
    107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Divided Measured 4266.04 5843.51 1.36977
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 Squared 407289 263351 1.54656
    eap30 subunit of ell complex. [refseq;acc:nm_007241] SNF8 Subtracted Ranked 209.299 249.187 39.888
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 Divided Rooted 60.875 77.7152 1.27664
    homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 Ranked 252.309 201.998 1.24907
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] RGL1 Subtracted Squared 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
    108 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 Divided Measured 4366.44 5899.76 1.35116
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 Ranked 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 Divided Squared 19321 12542.6 1.54043
    ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] RALGDS Subtracted Measured 14021.4 11523 2498.4
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 Squared 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
    voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] CACNG2 Divided 49.2925 62.397 1.26585
    109 44050 protein. [refseq;acc:nm_178832] C10orf83 Subtracted Measured 17385.9 14889.2 2496.7
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] no value Squared 88432.6 58423.3 30009.3
    glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] GAD2 Ranked 209.299 249.187 39.888
    guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] GNB4 Divided 266.933 333.281 1.24856
    myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 Squared 19321 12542.6 1.54043
    nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] NDUFS4 Subtracted Rooted 30.8986 46.4619 15.5633
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Divided Measured 4366.44 5899.76 1.35116
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 Rooted 49.2923 62.3969 1.26585
    110 deltex 2. [refseq;acc:nm_020892] DTX2 Ranked 333.144 267.393 1.2459
    gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] NAPG Subtracted 209.299 249.187 39.888

    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/