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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 780 to 829 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		red
    		network_comparison
    		green
    98 KIAA1012 Divided 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
    SEPT10 Subtracted septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 36304.3 125883
    99 no value Divided melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Ranked 88.2482 1.24949 110.265
    Subtracted jun dimerization protein. [refseq;acc:nm_130469] 204.641 43.684 160.957
    BRP44 brain protein 44. [swissprot;acc:o95563] Squared 89182.8 36046.2 125229
    GPSM2 Divided mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 1.29028 36.9304
    SEPT7 Subtracted septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Measured 15999.1 3008 19007.1
    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 1.3705 3225.65
    TOB2 Subtracted tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Rooted 19.9625 15.8355 35.798
    WDR33 Divided 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
    FOSL2 Subtracted fos-related antigen 2. [swissprot;acc:p15408] Ranked 204.641 43.595 161.046
    MAGEA10 Divided melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 88.2482 1.24949 110.265
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 1.29028 36.9304
    SEPT6 Subtracted septin 6. [swissprot;acc:q14141] Measured 15959.9 2997.2 18957.1
    SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 89182.8 36046.2 125229
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Rooted 19.9625 15.8355 35.798
    101 CPSF2 Divided 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
    DAB2IP Subtracted dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Rooted 19.9625 15.8355 35.798
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked 204.641 43.59 161.051
    GNAO1 Divided 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
    SEPT4 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] Measured 14924.4 2730.8 17655.2
    SEPT6 septin 6. [swissprot;acc:q14141] Squared 88953.6 35900.4 124854
    102 CLP1 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 121200 35726.6 85473.4
    CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted 19.9625 15.8355 35.798
    FIP1L1 Divided fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared 214143 1.54798 138337
    FOSL1 Subtracted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 43.574 161.068
    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 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
    STAMBPL1 Subtracted associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Measured 11068 2559.5 8508.5
    103 no value 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] Squared 407289 1.54656 263351
    CHMP2A Subtracted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Measured 11068 2559.5 8508.5
    CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted 19.9625 15.8355 35.798
    CUL1 Divided 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
    JUNB Subtracted transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 42.276 158.868
    SYMPK symplekin. [swissprot;acc:q92797] Squared 124118 35449.2 88668.8
    TRO Divided 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
    CSTF2T Subtracted likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared 121579 34319.7 87259.3
    HOMER2 Divided 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

    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/