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 1601 to 1650 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    101 no value Divided raptor; p150 target of rapamycin (tor)-scaffold protein containing wd-repeats. [refseq;acc:nm_020761] Squared Low confidence 63526.9 1.16811 54384.3
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] High confidence 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
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence 68.4921 6.1956 74.6877
    F13A1 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Ranked 226.395 14.682 211.713
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence 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
    PANK3 Subtracted pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Measured Low confidence 10685.5 927.4 11612.9
    ROGDI Divided leucine zipper domain protein. [refseq;acc:nm_024589] Ranked 221.996 1.07579 238.82
    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 High confidence 14924.4 2730.8 17655.2
    SEPT6 septin 6. [swissprot;acc:q14141] Squared 88953.6 35900.4 124854
    SLC16A10 solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] Low confidence 63903.1 8887.1 72790.2
    SMYD1 Divided set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Measured 5752.65 1.10037 6330.03
    VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Rooted 69.1897 1.08881 75.3346
    102 CD109 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Squared 54707.9 1.16767 46852.3
    CLP1 Subtracted pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] High confidence 121200 35726.6 85473.4
    CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted 19.9625 15.8355 35.798
    DGKQ Divided diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Ranked Low confidence 229.556 1.07543 213.456
    Rooted 61.2565 1.08856 66.6812
    DVL2 Subtracted segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 68.5063 6.1843 74.6906
    FIP1L1 Divided fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared High confidence 214143 1.54798 138337
    FOSL1 Subtracted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 43.574 161.068
    HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared Low confidence 65137.2 8809.1 73946.3
    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] Ranked High confidence 88.2482 1.24949 110.265
    PANK2 Subtracted pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Measured Low confidence 10684.1 927.1 11611.2
    PSEN1 Divided presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] High confidence 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
    TEX28P2 Divided testis-specific protein tex28. [swissprot;acc:o15482] Low confidence 5060.92 1.10006 5567.34
    TGM1 Subtracted protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Ranked 226.395 14.682 211.713
    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 High confidence 407289 1.54656 263351
    BNC1 zinc finger protein basonuclin. [swissprot;acc:q01954] Low confidence 105225 1.16733 90141.3
    CHMP2A Subtracted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Measured High confidence 11068 2559.5 8508.5
    COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Ranked Low confidence 220.969 14.603 235.572
    CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted High confidence 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
    GOSR2 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Measured Low confidence 5060.92 1.10006 5567.34
    JUNB Subtracted transcription factor jun-b. [swissprot;acc:p17275] Ranked High confidence 201.144 42.276 158.868
    PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared Low confidence 62385.1 8789.1 53596
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Measured 12315 924.4 11390.6
    PTPRA Divided vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Ranked 203.948 1.07538 189.652
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Rooted 64.1217 1.087 69.7
    SYMPK Subtracted symplekin. [swissprot;acc:q92797] Squared High confidence 124118 35449.2 88668.8
    TRO Divided trophinin. [swissprot;acc:q12816] Ranked 88.2482 1.24949 110.265
    VPS33A Subtracted vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Rooted Low confidence 69.1897 6.1449 75.3346
    104 no value Divided jun dimerization protein. [refseq;acc:nm_130469] High confidence 60.8365 1.27758 77.7233
    ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Ranked Low confidence 219.277 1.07377 204.212

    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/