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 description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 780 to 829 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    98 LBX1 transcription factor lbx1. [swissprot;acc:p52954] Rooted High confidence 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
    PHF12 phd finger protein 12; phd zinc finger transcription factor. [refseq;acc:nm_020889] Squared Low confidence 61253.4 1.17845 51977.8
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured High confidence 2353.63 1.3705 3225.65
    SLC7A6 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Ranked Low confidence 200.497 1.0798 185.679
    99 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Measured 5752.65 1.10037 6330.03
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Ranked High confidence 88.2482 1.24949 110.265
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted Low confidence 68.5805 1.08931 74.7056
    EIF4B eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Ranked 200.497 1.0798 185.679
    GPSM2 mosaic protein lgn. [swissprot;acc:p81274] Rooted High confidence 47.6504 1.29028 36.9304
    RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Squared Low confidence 61163.4 1.17794 51924
    SKP1A 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] Measured High confidence 2353.63 1.3705 3225.65
    WDR33 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
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked 88.2482 1.24949 110.265
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 1.29028 36.9304
    SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 63.7749 1.08901 69.4515
    SLC7A9 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Ranked 200.497 1.0798 185.679
    SMYD2 set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Measured 5752.65 1.10037 6330.03
    TP53I3 tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Squared 70019.5 1.17533 82296.2
    101 no value raptor; p150 target of rapamycin (tor)-scaffold protein containing wd-repeats. [refseq;acc:nm_020761] 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
    GNAO1 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
    ROGDI leucine zipper domain protein. [refseq;acc:nm_024589] Low confidence 221.996 1.07579 238.82
    SMYD1 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
    DGKQ diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Ranked 229.556 1.07543 213.456
    Rooted 61.2565 1.08856 66.6812
    FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared High confidence 214143 1.54798 138337
    MAGED2 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 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
    TEX28P2 testis-specific protein tex28. [swissprot;acc:o15482] Measured Low confidence 5060.92 1.10006 5567.34
    103 no value 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
    CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured High confidence 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
    PTPRA 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
    TRO trophinin. [swissprot;acc:q12816] Ranked High confidence 88.2482 1.24949 110.265
    104 no value jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 1.27758 77.7233
    ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Ranked Low confidence 219.277 1.07377 204.212
    CPSF4 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] Squared 60910.8 1.16546 52263.5
    HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Ranked High confidence 252.371 1.24926 202.016
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Measured 4241.57 1.36996 5810.79

    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/