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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1580 to 1629 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    198 BRAF Rooted b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Subtracted 116.576 105.948 10.628
    FOXP3 Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 263.191 231.394 1.13741
    GAD1 Rooted glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 59.6399 51.9242 1.1486
    PTPRB Squared protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 71062.2 95488.6 1.34373
    STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Subtracted 42411.6 55802.1 13390.5
    199 CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
    EGFL8 Ranked palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Divided 242.735 276.059 1.13729
    LUC7L Rooted luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Subtracted 55.297 65.9236 10.6266
    MIP Measured lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 10639.8 12117.3 1477.5
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Divided 4916.8 3888.18 1.26455
    PRSS16 Squared thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 71062.2 95488.6 1.34373
    RPS11 Ranked 40s ribosomal protein s11. [swissprot;acc:p04643] Subtracted 241.399 267.088 25.689
    STT3B Rooted source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Divided 61.2893 70.3856 1.14842
    200 no value Ranked 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Subtracted 241.808 267.335 25.527
    AQP1 Measured aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 10635.3 12111.4 1476.1
    BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided 4808.79 6074.21 1.26315
    CCDC47 Squared gk001 protein. [refseq;acc:nm_020198] 71062.2 95488.6 1.34373
    EGFL7 Ranked egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 242.718 276.018 1.1372
    MAPKAPK3 Squared mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Subtracted 42411.6 55802.1 13390.5
    PPP2CA Rooted serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 63.5827 53.0856 10.4971
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 61.2893 70.3856 1.14842
    201 CCT4 Measured t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 4810.22 6075.04 1.26294
    CLSTN2 Squared calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 71033.4 95440.2 1.3436
    CPSF4 Rooted 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] Subtracted 138.375 127.926 10.449
    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 70.3856 1.14842
    MAPK14 Squared 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] Subtracted 42411.6 55802.1 13390.5
    RPL11 Ranked 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 267.346 25.518
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 240.133 211.382 1.13601
    SSR4 Measured translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 10603.5 12069.5 1466
    202 no value Rooted splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Divided 57.3527 65.7973 1.14724
    CHRNA4 Squared neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Subtracted 42411.6 55802.1 13390.5
    CLSTN1 Measured calsyntenin-1 precursor. [swissprot;acc:o94985] 10603.5 12069.5 1466
    CLSTN3 Squared calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Divided 71030.1 95434.8 1.34358
    KIAA1012 Rooted trs85 homolog. [swissprot;acc:q9y2l5] Subtracted 138.375 127.926 10.449
    NEDD9 Measured 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] Divided 4812.01 6076.09 1.26269
    RPS4Y2 Ranked 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 240.758 266.079 25.321
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 201.478 228.784 1.13553
    203 no value Measured 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] Subtracted 10603.5 12069.5 1466
    Ranked 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 240.758 266.078 25.32
    Squared hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Divided 20988.2 15632.1 1.34263
    Rooted transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 46.3291 53.1063 1.14628
    ATG12 Measured autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 9352.11 1.25723
    CHRNA3 Squared neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Subtracted 42411.6 55802.1 13390.5
    TBC1D10A Ranked ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Divided 201.515 228.752 1.13516
    WDR33 Rooted wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Subtracted 138.032 127.651 10.381
    204 no value Measured small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Divided 4512.19 5655.52 1.25339
    Rooted 55.8956 63.9636 1.14434
    CAPN2 Ranked 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] Subtracted 268.632 243.588 25.044
    CPSF1 Rooted cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 138.032 127.651 10.381
    PTPRB Measured protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 10603.5 12069.4 1465.9

    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/