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 [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 808 to 857 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    202 XKR7 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Subtracted Low confidence 178.507 168.371 10.136
    203 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] High confidence 240.758 266.078 25.32
    GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided Low confidence 211.506 222.243 1.05076
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] High confidence 201.515 228.752 1.13516
    TENC1 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Subtracted Low confidence 216.404 206.277 10.127
    204 CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] High confidence 268.632 243.588 25.044
    GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Divided Low confidence 211.484 222.196 1.05065
    TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] High confidence 201.515 228.752 1.13516
    UBE2E4P ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Subtracted Low confidence 203.933 214.059 10.126
    205 CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] High confidence 268.635 243.592 25.043
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Divided Low confidence 211.475 222.177 1.05061
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] High confidence 228.1 200.968 1.13501
    TIMM23 mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Subtracted Low confidence 220.722 210.645 10.077
    206 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided 211.457 222.138 1.05051
    FMO6P putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Subtracted 209.792 199.758 10.034
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Divided High confidence 228.085 201.006 1.13472
    RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] Subtracted 241.411 266.414 25.003
    207 ANAPC10 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Divided Low confidence 213.495 203.244 1.05044
    EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted High confidence 237.312 212.363 24.949
    FMO2 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Low confidence 209.782 199.761 10.021
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided High confidence 285.684 252.234 1.13261
    208 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Subtracted 240.782 265.717 24.935
    FMO3 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Low confidence 209.778 199.757 10.021
    FMO6P putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Divided 209.792 199.758 1.05023
    SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] High confidence 285.684 252.234 1.13261
    209 BCCIP brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Subtracted 240.782 265.717 24.935
    CCDC22 jm1 protein. [refseq;acc:nm_014008] Low confidence 216.308 206.292 10.016
    FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Divided High confidence 285.684 252.234 1.13261
    FMO3 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Low confidence 209.778 199.757 1.05017
    210 no value rna-binding protein. [refseq;acc:nm_019027] Subtracted High confidence 237.302 212.41 24.892
    CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Divided 285.684 252.234 1.13261
    FMO1 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Subtracted Low confidence 209.768 199.756 10.012
    FMO2 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Divided 209.782 199.761 1.05016
    211 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted High confidence 237.302 212.41 24.892
    FMO1 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Divided Low confidence 209.768 199.756 1.05012
    FMO4 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Subtracted 209.765 199.755 10.01
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Divided High confidence 285.684 252.234 1.13261
    212 CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Low confidence 211.383 221.976 1.05011
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Subtracted 201.43 191.43 10
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] High confidence 237.302 212.41 24.892
    213 FMO4 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Divided Low confidence 209.765 199.755 1.05011
    HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Subtracted High confidence 237.302 212.41 24.892
    NEGR1 a kindred of iglon. [refseq;acc:nm_173808] Low confidence 199.671 209.654 9.983
    PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided High confidence 210.693 186.95 1.127
    214 LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 1.12605
    MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Subtracted 241.282 266.12 24.838
    NMBR neuromedin-b receptor (nmb-r) (neuromedin-b-preferring bombesin receptor). [swissprot;acc:p28336] Low confidence 199.671 209.654 9.983
    OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Divided 206.583 196.743 1.05001
    215 no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] High confidence 112 126 1.125

    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/