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 Value Type description 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
    		Value Type
    		description
    		red
    		green
    		network_comparison
    94 Squared ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 84857.8 53402.4 1.58903
    Rooted chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 47.6504 36.9304 1.29028
    95 Measured 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] 2397.19 3343.62 1.39481
    Ranked melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 88.2482 110.265 1.24949
    Squared protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 256169 162517 1.57626
    Rooted regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 47.6504 36.9304 1.29028
    96 Measured lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 4110.14 5694.99 1.3856
    Ranked melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 88.2482 110.265 1.24949
    Squared atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 7744.68 4959.41 1.56161
    Rooted putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 47.6504 36.9304 1.29028
    97 Measured 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] 2820.51 3897.1 1.3817
    Ranked melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 88.2482 110.265 1.24949
    Squared 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] 227160 146079 1.55505
    Rooted 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] 47.6504 36.9304 1.29028
    98 Measured presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 2353.63 3225.65 1.3705
    Ranked melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 88.2482 110.265 1.24949
    Squared trs85 homolog. [swissprot;acc:q9y2l5] 227160 146079 1.55505
    Rooted transcription factor lbx1. [swissprot;acc:p52954] 47.6504 36.9304 1.29028
    99 Measured 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] 2353.63 3225.65 1.3705
    Ranked melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 88.2482 110.265 1.24949
    Squared wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 226186 145568 1.55382
    Rooted mosaic protein lgn. [swissprot;acc:p81274] 47.6504 36.9304 1.29028
    100 Measured 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] 2353.63 3225.65 1.3705
    Ranked melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 88.2482 110.265 1.24949
    Squared cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 226186 145568 1.55382
    Rooted regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 47.6504 36.9304 1.29028
    101 Measured cullin homolog 2 (cul-2). [swissprot;acc:q13617] 2353.63 3225.65 1.3705
    Ranked melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 88.2482 110.265 1.24949
    Squared cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 222655 143584 1.5507
    Rooted guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 47.6504 36.9304 1.29028
    102 Measured presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 2353.63 3225.65 1.3705
    Ranked 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] 88.2482 110.265 1.24949
    Squared fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 214143 138337 1.54798
    Rooted rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 47.6504 36.9304 1.29028
    103 Measured cullin homolog 1 (cul-1). [swissprot;acc:q13616] 2353.63 3225.65 1.3705
    Ranked trophinin. [swissprot;acc:q12816] 88.2482 110.265 1.24949
    Squared 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] 407289 263351 1.54656
    Rooted proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 60.8365 77.7233 1.27758
    104 Measured musashi 2 isoform a. [refseq;acc:nm_138962] 4241.57 5810.79 1.36996
    Ranked homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 252.371 202.016 1.24926
    Squared cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 407289 263351 1.54656
    Rooted jun dimerization protein. [refseq;acc:nm_130469] 60.8365 77.7233 1.27758
    105 Measured musashi 1. [refseq;acc:nm_002442] 4241.57 5810.79 1.36996
    Ranked guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 266.716 333.165 1.24914
    Squared cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 407289 263351 1.54656
    Rooted fos-related antigen 2. [swissprot;acc:p15408] 60.8675 77.7168 1.27682
    106 Measured nuclear protein ukp68. [refseq;acc:nm_024824] 4241.57 5810.79 1.36996
    Ranked ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 252.329 202.004 1.24913
    Squared cytohesin 4. [swissprot;acc:q9uia0] 407289 263351 1.54656
    Rooted protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 60.8692 77.7165 1.27678

    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
    - 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/