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 [...,...].
    Gene Rank description red Hugo Network Comparison Type Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 380 to 429 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		red
    		Hugo
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    48 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 66.6504 FOSB Rooted Low confidence 75.3798 1.13097
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 242.742 no value Ranked 217.217 1.11751
    t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 27.7254 PBK Rooted High confidence 44.0299 1.58807
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] 8313.02 BACH2 Measured Low confidence 9645.34 1.16027
    trophinin. [swissprot;acc:q12816] 82347.8 TRO Squared 61881.5 1.33073
    49 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 28994.2 STAMBPL1 High confidence 17134.8 1.69212
    beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 133 ARRB2 Ranked 105 1.26667
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 66.6623 FOSL1 Rooted Low confidence 75.3751 1.1307
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 122475 no value Squared 159767 1.30449
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 27.7254 KHDRBS3 Rooted High confidence 44.0299 1.58807
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 13470.1 MAP1LC3B Measured Low confidence 11654.4 1.1558
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 779.167 NEUROD6 High confidence 1390.33 1.78438
    t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] 225.438 TBX19 Ranked Low confidence 202.569 1.11289
    50 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 133 ARRB1 High confidence 105 1.26667
    carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 202.235 CPD Rooted Low confidence 178.965 1.13003
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 122475 HOXB4 Squared 159767 1.30449
    junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 234.802 JPH3 Ranked 260.98 1.11149
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 27.7254 KHDRBS1 Rooted High confidence 44.0299 1.58807
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 13466.8 MAP1LC3A Measured Low confidence 11652.4 1.15571
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 779.167 NEUROD1 High confidence 1390.33 1.78438
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 28994.2 CHMP2A Squared 17134.8 1.69212
    51 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP
    dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] 7563.09 XKR7 Measured Low confidence 8732.2 1.15458
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 122475 HOXC5 Squared 159767 1.30449
    junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 234.802 JPH2 Ranked 260.98 1.11149
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 27.7254 KHDRBS2 Rooted High confidence 44.0299 1.58807
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 779.167 NEUROD4 Measured 1390.33 1.78438
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] 55.0884 GBAS Rooted Low confidence 62.0722 1.12677
    spermatogenesis associated 6. [refseq;acc:nm_019073] 133 SPATA6 Ranked High confidence 105 1.26667
    52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 779.167 CHD5 Measured 1390.33 1.78438
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 13195.9 ATG4B Low confidence 11486.4 1.14883
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 122475 no value Squared 159767 1.30449
    neuralized-like. [refseq;acc:nm_004210] 27.9107 NEURL Rooted High confidence 44.1656 1.58239
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 28994.2 VPS24 Squared 17134.8 1.69212
    nipsnap1 protein. [swissprot;acc:q9bpw8] 55.133 NIPSNAP1 Rooted Low confidence 62.1073 1.1265
    sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 234.802 SMPD2 Ranked 260.98 1.11149
    53 bcl2-related ovarian killer. [refseq;acc:nm_032515] 4955.33 BOK Measured 5659.35 1.14207
    cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 779.167 CDK2AP1 High confidence 1390.33 1.78438
    db83 protein. [swissprot;acc:p57088] 234.802 TMEM33 Ranked Low confidence 260.98 1.11149
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 122475 HOXD4 Squared 159767 1.30449
    nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 30.8986 NDUFS4 Rooted High confidence 46.4619 1.50369
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] 28994.2 CHMP4A Squared 17134.8 1.69212
    transcription factor jun-b. [swissprot;acc:p17275] 201.144 JUNB Ranked 158.868 1.26611
    transcription factor jun-d. [swissprot;acc:p17535] 67.1245 JUND Rooted Low confidence 75.5619 1.1257
    54 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 267.448 CPEB3 Ranked 240.822 1.11056
    deltex 2. [refseq;acc:nm_020892] 1618.84 DTX2 Measured High confidence 2651.88 1.63814
    homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 122475 HOXB5 Squared Low confidence 159767 1.30449
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 219048 MAGED4 High confidence 129762 1.68808
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 40.0958 UFC1 Rooted 58.7986 1.46645

    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/