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 Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 401 to 450 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    51 Measured dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] XKR7 Low confidence 1.15458 7563.09 8732.2
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 High confidence 1.78438 779.167 1390.33
    Ranked junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Low confidence 1.11149 234.802 260.98
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 High confidence 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] HOXC5 Low confidence 1.30449 122475 159767
    Rooted kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2 High confidence 1.58807 27.7254 44.0299
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS Low confidence 1.12677 55.0884 62.0722
    52 Measured chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 High confidence 1.78438 779.167 1390.33
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B Low confidence 1.14883 13195.9 11486.4
    Ranked amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2 High confidence 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] SMPD2 Low confidence 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] VPS24 High confidence 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] NIPSNAP1 Low confidence 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] CDK2AP1 High confidence 1.78438 779.167 1390.33
    Ranked db83 protein. [swissprot;acc:p57088] TMEM33 Low confidence 1.11149 234.802 260.98
    transcription factor jun-b. [swissprot;acc:p17275] JUNB High confidence 1.26611 201.144 158.868
    Squared homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Low confidence 1.30449 122475 159767
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A High confidence 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] JUND Low confidence 1.1257 67.1245 75.5619
    54 Measured deltex 2. [refseq;acc:nm_020892] DTX2 High confidence 1.63814 1618.84 2651.88
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] SEPT8 Low confidence 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] JUND High confidence 1.26425 200.941 158.941
    Squared homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Low confidence 1.30449 122475 159767
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 High confidence 1.68808 219048 129762
    Rooted protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 1.46645 40.0958 58.7986
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Low confidence 1.12566 67.118 75.5523
    55 Measured deltex homolog 1; hdx-1. [refseq;acc:nm_004416] DTX1 High confidence 1.63399 1629.21 2662.12
    septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 Low confidence 1.13694 13081.2 14872.6
    Ranked cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 1.11046 267.376 240.78
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] PRKRAP1 High confidence 1.26134 320.927 254.434
    Squared hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 1.68808 219048 129762
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Low confidence 1.30449 122475 159767
    Rooted 60s ribosomal protein l37a. [swissprot;acc:p12751] no value 1.12402 57.2649 64.3669
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 High confidence 1.44038 41.6734 28.9323
    56 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value Low confidence 1.13635 15464.1 17572.7
    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 High confidence 1.63302 1631.67 2664.55
    Ranked brachyury protein (t protein). [swissprot;acc:o15178] T Low confidence 1.11022 224.922 202.592
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] no value High confidence 1.25998 266.856 336.233
    Squared homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 1.30449 122475 159767
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence 1.68808 219048 129762
    Rooted ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 Low confidence 1.12389 62.7951 70.575
    cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] CTH High confidence 1.43986 41.6851 28.9509
    57 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Low confidence 1.13635 15464.1 17572.7
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3 High confidence 1.63302 1631.67 2664.55

    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/