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 Interaction Map Network Comparison Type red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 844 to 893 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    106 NOSTRIN nostrin. [refseq;acc:nm_052946] Ranked Subtracted 209.299 249.187 39.888
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted 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
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Measured Divided 4241.57 5810.79 1.36996
    107 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
    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 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
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Subtracted 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 no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared Divided 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
    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] Squared 78383 108483 30100
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Ranked 209.299 249.187 39.888
    109 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
    CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Rooted Divided 49.2923 62.3969 1.26585
    GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Ranked Subtracted 209.299 249.187 39.888
    GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Divided 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
    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 Subtracted 30.8986 46.4619 15.5633
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Measured Divided 4366.44 5899.76 1.35116
    110 no value pnas-18. [sptrembl;acc:q9bzu3] Squared Subtracted 87787.3 58155.8 29631.5
    CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Rooted Divided 49.293 62.3973 1.26585
    DTX2 deltex 2. [refseq;acc:nm_020892] Ranked 333.144 267.393 1.2459
    JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Rooted Subtracted 33.9632 18.4255 15.5377
    MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared Divided 19321 12542.6 1.54043
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Ranked Subtracted 209.299 249.187 39.888
    PPP1R8 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Measured 17385.9 14889.2 2496.7
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided 4366.44 5899.76 1.35116
    111 ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Squared Subtracted 79779.8 108084 28304.2
    CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Rooted Divided 49.2923 62.3969 1.26585
    CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured Subtracted 12365.2 14824.9 2459.7
    DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Ranked Divided 332.925 267.274 1.24563
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 209.299 249.187 39.888
    JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Rooted 33.9632 18.4255 15.5377
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Squared Divided 19321 12542.6 1.54043
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Measured 4366.44 5899.76 1.35116
    112 ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Subtracted 11757.8 9352.11 2405.69
    CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Rooted Divided 49.3267 62.4167 1.26537
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Squared Subtracted 96730.5 69286.7 27443.8
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Divided 19321 12542.6 1.54043
    PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Ranked 332.874 267.246 1.24557

    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/