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 Value Type Network Comparison Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 780 to 829 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		Network Comparison Type
    		description
    		red
    		green
    		network_comparison
    98 KIAA1012 Squared Divided trs85 homolog. [swissprot;acc:q9y2l5] 227160 146079 1.55505
    LBX1 Rooted transcription factor lbx1. [swissprot;acc:p52954] 47.6504 36.9304 1.29028
    MAGEA4 Ranked melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 88.2482 110.265 1.24949
    PSEN2 Measured presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 2353.63 3225.65 1.3705
    SEPT10 Squared Subtracted septin 10 isoform 1. [refseq;acc:nm_144710] 89578.7 125883 36304.3
    99 no value Ranked Divided melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 88.2482 110.265 1.24949
    Subtracted jun dimerization protein. [refseq;acc:nm_130469] 204.641 160.957 43.684
    BRP44 Squared brain protein 44. [swissprot;acc:o95563] 89182.8 125229 36046.2
    GPSM2 Rooted Divided mosaic protein lgn. [swissprot;acc:p81274] 47.6504 36.9304 1.29028
    SEPT7 Measured Subtracted septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 15999.1 19007.1 3008
    SKP1A Divided 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
    TOB2 Rooted Subtracted tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 19.9625 35.798 15.8355
    WDR33 Squared Divided wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 226186 145568 1.55382
    100 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
    FBXW7 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
    FOSL2 Ranked Subtracted fos-related antigen 2. [swissprot;acc:p15408] 204.641 161.046 43.595
    MAGEA10 Divided melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 88.2482 110.265 1.24949
    RGS17 Rooted regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 47.6504 36.9304 1.29028
    SEPT6 Measured Subtracted septin 6. [swissprot;acc:q14141] 15959.9 18957.1 2997.2
    SEPT7 Squared septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 89182.8 125229 36046.2
    TOB1 Rooted tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 19.9625 35.798 15.8355
    101 CPSF2 Squared Divided cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 222655 143584 1.5507
    CUL2 Measured cullin homolog 2 (cul-2). [swissprot;acc:q13617] 2353.63 3225.65 1.3705
    DAB2IP Rooted Subtracted dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 19.9625 35.798 15.8355
    FOSB Ranked protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 204.641 161.051 43.59
    GNAO1 Rooted Divided guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 47.6504 36.9304 1.29028
    MAGEB4 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
    SEPT4 Measured Subtracted 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] 14924.4 17655.2 2730.8
    SEPT6 Squared septin 6. [swissprot;acc:q14141] 88953.6 124854 35900.4
    102 CLP1 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 121200 85473.4 35726.6
    CPEB4 Rooted cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 19.9625 35.798 15.8355
    FIP1L1 Squared Divided fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 214143 138337 1.54798
    FOSL1 Ranked Subtracted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 204.642 161.068 43.574
    MAGED2 Divided 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
    PSEN1 Measured presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 2353.63 3225.65 1.3705
    RAP1GAP Rooted rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 47.6504 36.9304 1.29028
    STAMBPL1 Measured Subtracted associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 2559.5
    103 no value Squared Divided 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
    CHMP2A Measured Subtracted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 11068 8508.5 2559.5
    CPEB3 Rooted cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 19.9625 35.798 15.8355
    CUL1 Measured Divided cullin homolog 1 (cul-1). [swissprot;acc:q13616] 2353.63 3225.65 1.3705
    FOS Rooted proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 60.8365 77.7233 1.27758
    JUNB Ranked Subtracted transcription factor jun-b. [swissprot;acc:p17275] 201.144 158.868 42.276
    SYMPK Squared symplekin. [swissprot;acc:q92797] 124118 88668.8 35449.2
    TRO Ranked Divided trophinin. [swissprot;acc:q12816] 88.2482 110.265 1.24949
    104 no value Rooted jun dimerization protein. [refseq;acc:nm_130469] 60.8365 77.7233 1.27758
    CSTF2T Squared Subtracted likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 121579 87259.3 34319.7
    HOMER2 Ranked Divided homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 252.371 202.016 1.24926
    MSI2 Measured musashi 2 isoform a. [refseq;acc:nm_138962] 4241.57 5810.79 1.36996
    PSCD1 Squared cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 407289 263351 1.54656

    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/