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 description Network Comparison Type Hugo Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 758 to 807 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Value Type
    		red
    		network_comparison
    		green
    95 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Divided RGS19 Rooted 47.6504 1.29028 36.9304
    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 1.39481 3343.62
    tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Subtracted TP53BP2 Squared 123324 37046.1 86277.9
    96 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Divided no value 7744.68 1.56161 4959.41
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Subtracted ATF3 Ranked 201.949 48.278 153.671
    guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 Rooted 40.28 15.91 24.37
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided LASS2 Measured 4110.14 1.3856 5694.99
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 Ranked 88.2482 1.24949 110.265
    putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] RBM15 Rooted 47.6504 1.29028 36.9304
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted SEPT8 Measured 16177.9 3057.5 19235.4
    Squared 90226 36713 126939
    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] Divided APBA1 Measured 2820.51 1.3817 3897.1
    Subtracted Ranked 271.752 46.072 225.68
    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] Divided CPSF4 Squared 227160 1.55505 146079
    cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted CSTF2 126408 36467.5 89940.5
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] GNAI1 Rooted 40.2797 15.9092 24.3705
    melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided MAGEC1 Ranked 88.2482 1.24949 110.265
    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 1.29028 36.9304
    septin 10 isoform 1. [refseq;acc:nm_144710] Subtracted SEPT10 Measured 16067.4 3027 19094.4
    98 brain protein 44. [swissprot;acc:o95563] BRP44 15999.1 3008 19007.1
    guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3 Rooted 40.2797 15.9092 24.3705
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided MAGEA4 Ranked 88.2482 1.24949 110.265
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] PSEN2 Measured 2353.63 1.3705 3225.65
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Subtracted FOS Ranked 204.641 43.684 160.957
    septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 Squared 89578.7 36304.3 125883
    transcription factor lbx1. [swissprot;acc:p52954] Divided LBX1 Rooted 47.6504 1.29028 36.9304
    trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 Squared 227160 1.55505 146079
    99 brain protein 44. [swissprot;acc:o95563] Subtracted BRP44 89182.8 36046.2 125229
    jun dimerization protein. [refseq;acc:nm_130469] no value Ranked 204.641 43.684 160.957
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 88.2482 1.24949 110.265
    mosaic protein lgn. [swissprot;acc:p81274] GPSM2 Rooted 47.6504 1.29028 36.9304
    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 1.3705 3225.65
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Subtracted SEPT7 15999.1 3008 19007.1
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 Rooted 19.9625 15.8355 35.798
    wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Divided WDR33 Squared 226186 1.55382 145568
    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 1.3705 3225.65
    fos-related antigen 2. [swissprot;acc:p15408] Subtracted FOSL2 Ranked 204.641 43.595 161.046
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided MAGEA10 88.2482 1.24949 110.265
    regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] RGS17 Rooted 47.6504 1.29028 36.9304
    septin 6. [swissprot;acc:q14141] Subtracted SEPT6 Measured 15959.9 2997.2 18957.1
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 Squared 89182.8 36046.2 125229
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] TOB1 Rooted 19.9625 15.8355 35.798
    101 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided CPSF2 Squared 222655 1.5507 143584
    cullin homolog 2 (cul-2). [swissprot;acc:q13617] CUL2 Measured 2353.63 1.3705 3225.65
    dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Subtracted DAB2IP Rooted 19.9625 15.8355 35.798
    guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Divided GNAO1 47.6504 1.29028 36.9304
    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 1.24949 110.265
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted FOSB 204.641 43.59 161.051
    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] SEPT4 Measured 14924.4 2730.8 17655.2

    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/