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 Hugo Network Comparison Type red Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 375 to 424 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    47 nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] NFE2L2 8313.02 Measured Low confidence 9645.34 1.16027
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value 98517.9 Squared High confidence 56927.2 1.73059
    48 doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 779.167 Measured 1390.33 1.78438
    gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] GABARAP 65.4586 Ranked 83.0461 1.26868
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 6300.2 Squared 10703.5 1.69891
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB 66.6504 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] no value 242.742 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] PBK 27.7254 Rooted High confidence 44.0299 1.58807
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] BACH2 8313.02 Measured Low confidence 9645.34 1.16027
    trophinin. [swissprot;acc:q12816] TRO 82347.8 Squared 61881.5 1.33073
    49 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 28994.2 High confidence 17134.8 1.69212
    beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 133 Ranked 105 1.26667
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 66.6623 Rooted Low confidence 75.3751 1.1307
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value 122475 Squared 159767 1.30449
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3 27.7254 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] MAP1LC3B 13470.1 Measured Low confidence 11654.4 1.1558
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 779.167 High confidence 1390.33 1.78438
    t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] TBX19 225.438 Ranked Low confidence 202.569 1.11289
    50 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 133 High confidence 105 1.26667
    carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] CPD 202.235 Rooted Low confidence 178.965 1.13003
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 122475 Squared 159767 1.30449
    junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 234.802 Ranked 260.98 1.11149
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1 27.7254 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] MAP1LC3A 13466.8 Measured Low confidence 11652.4 1.15571
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 779.167 High confidence 1390.33 1.78438
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] CHMP2A 28994.2 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] XKR7 7563.09 Measured Low confidence 8732.2 1.15458
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 122475 Squared 159767 1.30449
    junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 234.802 Ranked 260.98 1.11149
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2 27.7254 Rooted High confidence 44.0299 1.58807
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 779.167 Measured 1390.33 1.78438
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS 55.0884 Rooted Low confidence 62.0722 1.12677
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 133 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] CHD5 779.167 Measured 1390.33 1.78438
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B 13195.9 Low confidence 11486.4 1.14883
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value 122475 Squared 159767 1.30449
    neuralized-like. [refseq;acc:nm_004210] NEURL 27.9107 Rooted High confidence 44.1656 1.58239
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 28994.2 Squared 17134.8 1.69212
    nipsnap1 protein. [swissprot;acc:q9bpw8] NIPSNAP1 55.133 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] SMPD2 234.802 Ranked 260.98 1.11149
    53 bcl2-related ovarian killer. [refseq;acc:nm_032515] BOK 4955.33 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] CDK2AP1 779.167 High confidence 1390.33 1.78438
    db83 protein. [swissprot;acc:p57088] TMEM33 234.802 Ranked Low confidence 260.98 1.11149
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 122475 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] NDUFS4 30.8986 Rooted High confidence 46.4619 1.50369
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A 28994.2 Squared 17134.8 1.69212
    transcription factor jun-b. [swissprot;acc:p17275] JUNB 201.144 Ranked 158.868 1.26611
    transcription factor jun-d. [swissprot;acc:p17535] JUND 67.1245 Rooted Low confidence 75.5619 1.1257

    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/