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 Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 375 to 424 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		network_comparison
    		green
    94 RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Rooted 47.6504 1.29028 36.9304
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared 84857.8 1.58903 53402.4
    95 MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked 88.2482 1.24949 110.265
    PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Squared 256169 1.57626 162517
    RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Rooted 47.6504 1.29028 36.9304
    SON 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] Measured 2397.19 1.39481 3343.62
    96 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Squared 7744.68 1.56161 4959.41
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured 4110.14 1.3856 5694.99
    MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked 88.2482 1.24949 110.265
    RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Rooted 47.6504 1.29028 36.9304
    97 APBA1 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] Measured 2820.51 1.3817 3897.1
    CPSF4 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] Squared 227160 1.55505 146079
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked 88.2482 1.24949 110.265
    RGS20 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] Rooted 47.6504 1.29028 36.9304
    98 KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Squared 227160 1.55505 146079
    LBX1 transcription factor lbx1. [swissprot;acc:p52954] Rooted 47.6504 1.29028 36.9304
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked 88.2482 1.24949 110.265
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured 2353.63 1.3705 3225.65
    99 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Ranked 88.2482 1.24949 110.265
    GPSM2 mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 1.29028 36.9304
    SKP1A 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] Measured 2353.63 1.3705 3225.65
    WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Squared 226186 1.55382 145568
    100 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
    FBXW7 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] Measured 2353.63 1.3705 3225.65
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked 88.2482 1.24949 110.265
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 1.29028 36.9304
    101 CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared 222655 1.5507 143584
    CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 1.3705 3225.65
    GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Rooted 47.6504 1.29028 36.9304
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Ranked 88.2482 1.24949 110.265
    102 FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared 214143 1.54798 138337
    MAGED2 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] Ranked 88.2482 1.24949 110.265
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured 2353.63 1.3705 3225.65
    RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted 47.6504 1.29028 36.9304
    103 no value 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] Squared 407289 1.54656 263351
    CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured 2353.63 1.3705 3225.65
    FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Rooted 60.8365 1.27758 77.7233
    TRO trophinin. [swissprot;acc:q12816] Ranked 88.2482 1.24949 110.265
    104 no value jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 1.27758 77.7233
    HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Ranked 252.371 1.24926 202.016
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Measured 4241.57 1.36996 5810.79
    PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared 407289 1.54656 263351
    105 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Rooted 60.8675 1.27682 77.7168
    GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Ranked 266.716 1.24914 333.165
    MSI1 musashi 1. [refseq;acc:nm_002442] Measured 4241.57 1.36996 5810.79
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared 407289 1.54656 263351
    106 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Ranked 252.329 1.24913 202.004
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 1.27678 77.7165
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Squared 407289 1.54656 263351
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Measured 4241.57 1.36996 5810.79

    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/