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 description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1413 to 1462 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    354 GATAD2B Measured transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 12839 10911.1 1.17669
    PSPC1 Squared paraspeckle protein 1. [refseq;acc:nm_018282] 71360.3 57385.8 1.24352
    STX10 Ranked syntaxin 10 (syn10). [swissprot;acc:o60499] 234.691 257.442 1.09694
    WDR12 Rooted wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 49.2848 54.5246 1.10632
    355 no value Measured tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 12839 10911.1 1.17669
    PRSS7 Rooted enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 58.0752 64.23 1.10598
    STX6 Ranked syntaxin 6. [swissprot;acc:o43752] 234.673 257.414 1.09691
    UNC84A Squared sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 15588.1 19381.8 1.24337
    356 no value Ranked 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796 1.09684
    SF3B2 Rooted splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 58.0752 64.23 1.10598
    SH3GL3 Squared sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 35247.5 43820.5 1.24322
    TCP1 Measured t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 11004.2 12944.2 1.1763
    357 no value Ranked 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 243.12 266.661 1.09683
    GRB2 Rooted growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 61.2684 67.755 1.10587
    IMMP2L Measured imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 5061.11 5950.22 1.17567
    PPP2R2D Squared uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 9811.86 7908.29 1.24071
    358 no value Measured microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 5061.11 5950.22 1.17567
    Squared serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 9811.73 7908.13 1.24071
    NEK2 Rooted serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] 61.2684 67.755 1.10587
    RPL10L Ranked ribosomal protein l10-like protein. [refseq;acc:nm_080746] 243.12 266.662 1.09683
    359 CDK3 Measured cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 12798.9 10887.2 1.17559
    PES1 Rooted pescadillo homolog 1. [swissprot;acc:o00541] 49.2488 54.4603 1.10582
    PPP2R2B Squared serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 9812.34 7908.87 1.24068
    RPL4 Ranked 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 239.277 262.434 1.09678
    360 CCNB2 Measured g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 12796.8 10886 1.17553
    GNL3 Rooted nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 49.3771 54.5905 1.10558
    PPP2R2C Squared serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 9814.47 7911.48 1.24054
    SEC61G Ranked protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] 243.072 266.559 1.09663
    361 CDK2 Measured cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 12787.6 10880.5 1.17528
    MRPL17 Ranked mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] 242.83 266.248 1.09644
    RPS4Y2 Rooted 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 50.7801 45.9472 1.10518
    SFPQ Squared splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] 70694.1 56989.9 1.24047
    362 no value Rooted 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 50.7803 45.9477 1.10518
    CCNB1 Measured g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 12786.6 10879.9 1.17525
    SHROOM2 Ranked apical-like protein (apxl protein). [swissprot;acc:q13796] 231.492 211.136 1.09641
    TAF7 Squared transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 57808.9 46630.3 1.23973
    363 BOP1 Rooted block of proliferation 1. [swissprot;acc:q14137] 49.4884 54.6735 1.10477
    CDC2 Measured cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 12780.7 10876.4 1.17509
    SHROOM3 Ranked shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 231.481 211.131 1.09639
    TAF7L Squared tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] 57579.2 46497.2 1.23834
    364 DDX31 Rooted dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 50.0785 55.3215 1.1047
    GULP1 Measured ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] 5189 6088.47 1.17334
    POLR2B Ranked dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 243.208 266.617 1.09625
    SH2D3C Squared sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 17957.2 22234.1 1.23817
    365 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 17965.8 22243 1.23807
    CAPS Measured calcyphosine. [swissprot;acc:q13938] 5189 6088.47 1.17334
    MRPL36 Ranked 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 242.744 266.07 1.09609
    NOL1 Rooted proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 49.7541 54.9425 1.10428
    366 BHLHB4 Squared ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 62783.5 50784.1 1.23628
    CRNKL1 Measured crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 5189 6088.47 1.17334

    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/