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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 375 to 424 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    94 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value Ranked 88.2482 110.265 1.24949
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] RGL1 Squared 84857.8 53402.4 1.58903
    95 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 Ranked 88.2482 110.265 1.24949
    protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] PPP1R7 Squared 256169 162517 1.57626
    regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] RGS19 Rooted 47.6504 36.9304 1.29028
    son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] SON Measured 2397.19 3343.62 1.39481
    96 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value Squared 7744.68 4959.41 1.56161
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 Measured 4110.14 5694.99 1.3856
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 Ranked 88.2482 110.265 1.24949
    putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] RBM15 Rooted 47.6504 36.9304 1.29028
    97 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] APBA1 Measured 2820.51 3897.1 1.3817
    cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] CPSF4 Squared 227160 146079 1.55505
    melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Ranked 88.2482 110.265 1.24949
    regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] RGS20 Rooted 47.6504 36.9304 1.29028
    98 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Ranked 88.2482 110.265 1.24949
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] PSEN2 Measured 2353.63 3225.65 1.3705
    transcription factor lbx1. [swissprot;acc:p52954] LBX1 Rooted 47.6504 36.9304 1.29028
    trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 Squared 227160 146079 1.55505
    99 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value Ranked 88.2482 110.265 1.24949
    mosaic protein lgn. [swissprot;acc:p81274] GPSM2 Rooted 47.6504 36.9304 1.29028
    s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] SKP1A Measured 2353.63 3225.65 1.3705
    wd-repeat protein wdc146. [swissprot;acc:q9c0j8] WDR33 Squared 226186 145568 1.55382
    100 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] CPSF1
    f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] FBXW7 Measured 2353.63 3225.65 1.3705
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Ranked 88.2482 110.265 1.24949
    regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] RGS17 Rooted 47.6504 36.9304 1.29028
    101 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] CPSF2 Squared 222655 143584 1.5507
    cullin homolog 2 (cul-2). [swissprot;acc:q13617] CUL2 Measured 2353.63 3225.65 1.3705
    guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] GNAO1 Rooted 47.6504 36.9304 1.29028
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Ranked 88.2482 110.265 1.24949
    102 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 Squared 214143 138337 1.54798
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Ranked 88.2482 110.265 1.24949
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 Measured 2353.63 3225.65 1.3705
    rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] RAP1GAP Rooted 47.6504 36.9304 1.29028
    103 cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1 Measured 2353.63 3225.65 1.3705
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] no value Squared 407289 263351 1.54656
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] FOS Rooted 60.8365 77.7233 1.27758
    trophinin. [swissprot;acc:q12816] TRO Ranked 88.2482 110.265 1.24949
    104 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 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
    musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 Measured 4241.57 5810.79 1.36996
    105 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 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
    106 cytohesin 4. [swissprot;acc:q9uia0] PSCD4 Squared 407289 263351 1.54656
    nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 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
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 Ranked 252.329 202.004 1.24913

    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/