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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 582 to 631 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		green
    		network_comparison
    582 homeobox protein barh-like 1. [swissprot;acc:q9hbu1] 237.28 252.492 1.06411
    583 opsin 4 (melanopsin). [swissprot;acc:q9uhm6]
    584 t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]
    585 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
    586 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
    587 homeobox protein barh-like 2. [swissprot;acc:q9umq3]
    588 shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] 216.557 230.362 1.06375
    589 u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 228.215 214.546 1.06371
    590 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 217.215 204.279 1.06333
    591 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] 216.72 230.439 1.0633
    592 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 91.63 97.4011 1.06298
    593 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 232.118 218.406 1.06278
    594 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 1.06256
    595 vav proto-oncogene. [swissprot;acc:p15498] 212.2 199.849 1.0618
    596 vav-3 protein. [swissprot;acc:q9ukw4] 212.253 199.908 1.06175
    597 vav-2 protein. [swissprot;acc:p52735] 212.526 200.212 1.0615
    598 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 248.463 234.095 1.06138
    599 rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]
    600 rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]
    601 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] 206.274 218.792 1.06069
    602 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
    603 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 225.829 212.945 1.0605
    604 60s ribosomal protein l15. [swissprot;acc:p39030] 217.862 230.978 1.0602
    605 histone h2b.c (h2b/c). [swissprot;acc:q99880] 247.47 233.441 1.0601
    606 histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
    607 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
    608 histone h2b. [refseq;acc:nm_175055]
    609 histone h2b.s (h2b/s). [swissprot;acc:p57053]
    610 histone h2b.d (h2b/d). [swissprot;acc:q99877]
    611 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]
    612 testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
    613 histone h2b.e (h2b/e). [swissprot;acc:q99879]
    614 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 214.257 202.125 1.06002
    615 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 202.132 1.05999
    616 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
    617 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 202.135 1.05997
    618 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 214.256 202.139 1.05994
    619 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
    620 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 202.14
    621 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
    622 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
    623 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]
    624 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 202.139
    625 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 202.14
    626 gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
    627 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 202.139
    628 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 202.14
    629 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
    630 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 202.141 1.05993
    631 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]

    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/