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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 830 to 879 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    104 Subtracted RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted 19.9625 35.798 15.8355
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Measured 11068 8508.5 2559.5
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Ranked 256.228 298.438 42.21
    105 Divided FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Rooted 60.8675 77.7168 1.27682
    GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Ranked 266.716 333.165 1.24914
    MSI1 musashi 1. [refseq;acc:nm_002442] Measured 4241.57 5810.79 1.36996
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared 407289 263351 1.54656
    Subtracted no value 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] Rooted 63.7477 48.1588 15.5889
    JUND transcription factor jun-d. [swissprot;acc:p17535] Ranked 200.941 158.941 42
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 90432.9 56304.2 34128.7
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Measured 11068 8508.5 2559.5
    106 Divided COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Ranked 252.329 202.004 1.24913
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 1.27678
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Squared 407289 263351 1.54656
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Measured 4241.57 5810.79 1.36996
    Subtracted CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] 11068 8508.5 2559.5
    NOSTRIN nostrin. [refseq;acc:nm_052946] Ranked 209.299 249.187 39.888
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted 63.7477 48.1589 15.5888
    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] Squared 82624.3 115061 32436.7
    107 Divided FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted 60.875 77.7152 1.27664
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 201.998 1.24907
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Measured 4266.04 5843.51 1.36977
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Squared 407289 263351 1.54656
    Subtracted 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 63.7477 48.1594 15.5883
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared 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
    108 Divided no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared 19321 12542.6 1.54043
    CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Rooted 49.2925 62.397 1.26585
    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 4366.44 5899.76 1.35116
    HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked 252.296 201.995 1.24902
    Subtracted 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 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] Squared 78383 108483 30100
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Ranked 209.299 249.187 39.888
    109 Divided CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Rooted 49.2923 62.3969 1.26585
    GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Ranked 266.933 333.281 1.24856
    MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared 19321 12542.6 1.54043
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Measured 4366.44 5899.76 1.35116
    Subtracted no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared 88432.6 58423.3 30009.3
    C10orf83 44050 protein. [refseq;acc:nm_178832] Measured 17385.9 14889.2 2496.7
    GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Ranked 209.299 249.187 39.888
    NDUFS4 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] Rooted 30.8986 46.4619 15.5633
    110 Divided CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 49.293 62.3973 1.26585
    DTX2 deltex 2. [refseq;acc:nm_020892] Ranked 333.144 267.393 1.2459
    MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared 19321 12542.6 1.54043
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Measured 4366.44 5899.76 1.35116
    Subtracted no value pnas-18. [sptrembl;acc:q9bzu3] Squared 87787.3 58155.8 29631.5
    JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Rooted 33.9632 18.4255 15.5377
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Ranked 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/