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 [...,...].
    Filtered network_comparison green Value Type Gene Network Comparison Type Interaction Map red Rank description
    Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
    Filtered  : 0
    network_comparison
    green
    Value Type
    Network Comparison Type
    Interaction Map
    red
    Rank
    description
    0.9646 24.3289 Rooted Subtracted Low confidence 23.3643 593 40s ribosomal protein s12. [swissprot;acc:p25398]
    0.965708 1.63441 Squared High confidence 0.668702 447 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
    0.9672 17.4854 Rooted 16.5182 381 swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]
    0.9753 43.0082 42.0329 379 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]
    380 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
    0.9767 16.5084 Low confidence 15.5317 592 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]
    0.9771 33.4964 34.4735 591 neprilysin (ec 3.4.24.11) (neutral endopeptidase) (nep) (enkephalinase) (common acute lymphocytic leukemia antigen) (calla) (neutral endopeptidase 24.11) (cd10). [swissprot;acc:p08473]
    0.9803 19.119 18.1387 590 ba161i19.3 (similar to ribosomal protein l36). [sptrembl;acc:q8wx03]
    0.9827 25.6434 24.6607 589 rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]
    0.9843 19.2328 20.2171 588 kappa b-ras 1. [refseq;acc:nm_020345]
    0.9856 33.9829 34.9685 587 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]
    0.9892 26.8952 25.906 586 60s ribosomal protein l9. [swissprot;acc:p32969]
    0.98968 6.55744 High confidence 5.56776 378 methyltransferase like 2. [refseq;acc:nm_018396]
    0.9907 29.8694 30.8601 377 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
    0.995 26.0677 Low confidence 27.0627 585 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]
    1 0.00001 Measured Divided High confidence 0.00001 494 histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
    495 histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
    496 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
    497 histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
    498 translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
    499 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
    500 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
    501 h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
    502 brca1 associated protein. [refseq;acc:nm_006768]
    Low confidence 837 gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
    838 gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
    839 cobw-like protein. [refseq;acc:nm_018491]
    840 translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
    841 gamma-glutamyltransferase. [sptrembl;acc:q14390]
    842 gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
    843 gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
    Ranked High confidence 501 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
    502 brca1 associated protein. [refseq;acc:nm_006768]
    Low confidence 837 gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
    838 gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
    839 cobw-like protein. [refseq;acc:nm_018491]
    841 gamma-glutamyltransferase. [sptrembl;acc:q14390]
    842 gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
    843 gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
    Squared High confidence 494 histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
    495 histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
    496 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
    497 histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
    498 translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
    499 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
    500 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
    501 h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
    502 brca1 associated protein. [refseq;acc:nm_006768]
    Low confidence 837 gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
    838 gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]

    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
    - 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/