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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 382 to 431 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    48 Squared trophinin. [swissprot;acc:q12816] Low confidence TRO 1.33073 82347.8 61881.5
    Rooted protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB 1.13097 66.6504 75.3798
    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] High confidence PBK 1.58807 27.7254 44.0299
    49 Measured microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Low confidence MAP1LC3B 1.1558 13470.1 11654.4
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence NEUROD6 1.78438 779.167 1390.33
    Ranked beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 1.26667 133 105
    t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Low confidence TBX19 1.11289 225.438 202.569
    Squared associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence STAMBPL1 1.69212 28994.2 17134.8
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence no value 1.30449 122475 159767
    Rooted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 1.1307 66.6623 75.3751
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence KHDRBS3 1.58807 27.7254 44.0299
    50 Measured microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Low confidence MAP1LC3A 1.15571 13466.8 11652.4
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] High confidence NEUROD1 1.78438 779.167 1390.33
    Ranked beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 1.26667 133 105
    junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Low confidence JPH3 1.11149 234.802 260.98
    Squared homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 1.30449 122475 159767
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] High confidence CHMP2A 1.69212 28994.2 17134.8
    Rooted carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence CPD 1.13003 202.235 178.965
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence KHDRBS1 1.58807 27.7254 44.0299
    51 Measured dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Low confidence XKR7 1.15458 7563.09 8732.2
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence NEUROD4 1.78438 779.167 1390.33
    Ranked junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Low confidence JPH2 1.11149 234.802 260.98
    spermatogenesis associated 6. [refseq;acc:nm_019073] High confidence SPATA6 1.26667 133 105
    Squared associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP 1.69212 28994.2 17134.8
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence HOXC5 1.30449 122475 159767
    Rooted kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence KHDRBS2 1.58807 27.7254 44.0299
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] Low confidence GBAS 1.12677 55.0884 62.0722
    52 Measured chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence CHD5 1.78438 779.167 1390.33
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Low confidence ATG4B 1.14883 13195.9 11486.4
    Ranked amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] High confidence AMPD2 1.26667 133 105
    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] Low confidence SMPD2 1.11149 234.802 260.98
    Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value 1.30449 122475 159767
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence VPS24 1.69212 28994.2 17134.8
    Rooted neuralized-like. [refseq;acc:nm_004210] NEURL 1.58239 27.9107 44.1656
    nipsnap1 protein. [swissprot;acc:q9bpw8] Low confidence NIPSNAP1 1.1265 55.133 62.1073
    53 Measured bcl2-related ovarian killer. [refseq;acc:nm_032515] BOK 1.14207 4955.33 5659.35
    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] High confidence CDK2AP1 1.78438 779.167 1390.33
    Ranked db83 protein. [swissprot;acc:p57088] Low confidence TMEM33 1.11149 234.802 260.98
    transcription factor jun-b. [swissprot;acc:p17275] High confidence JUNB 1.26611 201.144 158.868
    Squared homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence HOXD4 1.30449 122475 159767
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] High confidence CHMP4A 1.69212 28994.2 17134.8
    Rooted 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 1.50369 30.8986 46.4619
    transcription factor jun-d. [swissprot;acc:p17535] Low confidence JUND 1.1257 67.1245 75.5619
    54 Measured deltex 2. [refseq;acc:nm_020892] High confidence DTX2 1.63814 1618.84 2651.88
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence SEPT8 1.13859 13203.5 15033.4
    Ranked cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 1.11056 267.448 240.822
    transcription factor jun-d. [swissprot;acc:p17535] High confidence JUND 1.26425 200.941 158.941
    Squared homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Low confidence HOXB5 1.30449 122475 159767
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] High confidence MAGED4 1.68808 219048 129762
    Rooted protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 1.46645 40.0958 58.7986

    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/