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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1601 to 1650 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    201 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured Divided 4810.22 1.26294 6075.04
    CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared 71033.4 1.3436 95440.2
    CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Rooted Subtracted 138.375 10.449 127.926
    DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Divided 61.2893 1.14842 70.3856
    MAPK14 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Squared Subtracted 42411.6 13390.5 55802.1
    RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Ranked 241.828 25.518 267.346
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 240.133 1.13601 211.382
    SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Measured Subtracted 10603.5 1466 12069.5
    202 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Rooted Divided 57.3527 1.14724 65.7973
    CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared Subtracted 42411.6 13390.5 55802.1
    CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985] Measured 10603.5 1466 12069.5
    CLSTN3 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared Divided 71030.1 1.34358 95434.8
    KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Rooted Subtracted 138.375 10.449 127.926
    NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Measured Divided 4812.01 1.26269 6076.09
    RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked Subtracted 240.758 25.321 266.079
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 201.478 1.13553 228.784
    203 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted 240.758 25.32 266.078
    hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Squared Divided 20988.2 1.34263 15632.1
    succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Measured Subtracted 10603.5 1466 12069.5
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Rooted Divided 46.3291 1.14628 53.1063
    ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Measured 11757.8 1.25723 9352.11
    CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Squared Subtracted 42411.6 13390.5 55802.1
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked Divided 201.515 1.13516 228.752
    WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Rooted Subtracted 138.032 10.381 127.651
    204 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Measured Divided 4512.19 1.25339 5655.52
    Rooted 55.8956 1.14434 63.9636
    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] Ranked Subtracted 268.632 25.044 243.588
    CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Rooted 138.032 10.381 127.651
    PTPRB protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Measured 10603.5 1465.9 12069.4
    SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Squared 42411.6 13390.5 55802.1
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Divided 12326.4 1.34045 16522.9
    TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked 201.515 1.13516 228.752
    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] Subtracted 268.635 25.043 243.592
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Divided 228.1 1.13501 200.968
    PRSS16 thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Measured Subtracted 10603.5 1465.9 12069.4
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Rooted 114.309 10.218 124.527
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Measured Divided 4512.19 1.25339 5655.52
    Rooted 55.8956 1.14434 63.9636
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Squared 12326.4 1.34045 16522.9
    TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Subtracted 40982.6 13289.7 54272.3
    206 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Measured Divided 5720.25 1.24965 4577.5
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Rooted 140.508 1.14348 122.878
    CCDC47 gk001 protein. [refseq;acc:nm_020198] Measured Subtracted 10603.5 1465.9 12069.4
    DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Squared Divided 12326.4 1.34045 16522.9
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Ranked 228.085 1.13472 201.006
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted Subtracted 45.4558 10.1437 55.5995
    RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] Ranked 241.411 25.003 266.414
    TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Squared 46739.9 12394.6 59134.5
    207 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Measured Divided 4771.21 1.24946 5961.43
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Rooted 140.508 1.14348 122.878

    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/