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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1280 to 1329 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 1715 HDC 206.549 203.844 1.01327
    histidine-rich membrane protein ke4. [swissprot;acc:q92504] 2718 SLC39A7 216.52 216.632 1.00052
    histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 1920 HARS 187.292 185.413 1.01013
    histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 1919 HARS2 187.231 185.349 1.01015
    histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 182 HAT1 277.546 240.461 1.15422
    histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 279 RBBP7 252.644 228.42 1.10605
    histone deacetylase 1 (hd1). [swissprot;acc:q13547] 777 HDAC1 225.989 215.53 1.04853
    histone deacetylase 11 (hd11). [swissprot;acc:q96db2] 2376 HDAC11 212.724 213.574 1.004
    histone deacetylase 2 (hd2). [swissprot;acc:q92769] 775 no value 226.003 215.541 1.04854
    histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379] 2813 HDAC3 0.00001 0.00001 1
    histone deacetylase 4 (hd4). [swissprot;acc:p56524] 2424 HDAC4 220.682 221.472 1.00358
    histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] 2423 HDAC5 221.471
    histone deacetylase 6 (hd6). [swissprot;acc:q9ubn7] 3152 HDAC6 0.00001 0.00001 1
    histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] 2425 HDAC9 220.682 221.472 1.00358
    histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001] 2784 HIST3H2A 0.00001 0.00001 1
    histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] 2767 no value
    histone h2a.e (h2a/e). [swissprot;acc:q99878] 2765
    histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777] 2769 HIST2H2AC
    histone h2a.x (h2a/x). [swissprot;acc:p16104] 2768 HIST2H2AB
    histone h2a; h2a histone family, member r. [refseq;acc:nm_170745] 2852 HIST1H2AA
    histone h2b. [refseq;acc:nm_175055] 608 no value 247.47 233.441 1.0601
    histone h2b.c (h2b/c). [swissprot;acc:q99880] 605 HIST1H2BL
    histone h2b.d (h2b/d). [swissprot;acc:q99877] 610 no value
    histone h2b.e (h2b/e). [swissprot;acc:q99879] 613
    histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 606 HIST2H2BA
    histone h2b.s (h2b/s). [swissprot;acc:p57053] 609 no value
    histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 607
    histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 723 244.842 232.577 1.05274
    histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 611 HIST3H3 247.47 233.441 1.0601
    histone h4. [swissprot;acc:p02304] 946 no value 227.765 219.902 1.03576
    histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] 1342 SUV39H1 226.433 231.491 1.02234
    histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] 1340 SUV39H2
    hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] 645 HTATSF1 217.67 230.596 1.05938
    hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 1503 KRR1 242.181 237.834 1.01828
    hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] 643 HRBL 217.67 230.596 1.05938
    hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] 1613 HTATIP2 182.378 185.241 1.0157
    hmg2 like. [refseq;acc:nm_145205] 2799 HMGB4 0.00001 0.00001 1
    homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] 2194 PROX1 209.54 208.162 1.00662
    homeobox protein barh-like 1. [swissprot;acc:q9hbu1] 582 BARX1 237.28 252.492 1.06411
    homeobox protein barh-like 2. [swissprot;acc:q9umq3] 587 BARX2
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 557 CUTL2 207.272 194.371 1.06637
    homeobox protein dlx-2. [swissprot;acc:q07687] 2337 DLX2 229.258 230.294 1.00452
    homeobox protein dlx-3. [swissprot;acc:o60479] 2340 DLX3
    homeobox protein dlx-5. [swissprot;acc:p56178] 2338 DLX5
    homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 1167 EN2 219.399 213.784 1.02626
    homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 7 HLX 215 322 1.49767
    homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 614 HOXA10 214.257 202.125 1.06002
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 686 no value 132.413 125.389 1.05602
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 685 HOXA5
    homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 616 HOXA9 214.257 202.132 1.05999

    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/