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 783 to 832 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    196 GAD2 Rooted glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 59.6399 51.9242 1.1486
    PPP2R5E Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 17738.5 13995.7 1.26742
    197 no value Squared 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] 71062.4 95488.9 1.34373
    FOXP1 Ranked forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 263.215 231.407 1.13745
    NAPG Rooted gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 59.6399 51.9242 1.1486
    PPP2R5A Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 17738.5 13995.7 1.26742
    198 BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 17710.9 13977.7 1.26708
    FOXP3 Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 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
    199 EGFL8 Ranked palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 242.735 276.059 1.13729
    PPP2CA Measured serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 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
    STT3B Rooted source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 61.2893 70.3856 1.14842
    200 BCAR1 Measured crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 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
    STT3A Rooted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 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
    DDOST Rooted 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] 61.2893 70.3856 1.14842
    SF4 Ranked splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 211.382 1.13601
    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] 57.3527 65.7973 1.14724
    CLSTN3 Squared calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 71030.1 95434.8 1.34358
    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] 4812.01 6076.09 1.26269
    TRPC4 Ranked short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 201.478 228.784 1.13553
    203 no value Squared hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 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
    TBC1D10A Ranked ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 201.515 228.752 1.13516
    204 no value Measured small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 4512.19 5655.52 1.25339
    Rooted 55.8956 63.9636 1.14434
    STT3B Squared source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 12326.4 16522.9 1.34045
    TRPC5 Ranked short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 201.515 228.752 1.13516
    205 LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 228.1 200.968 1.13501
    SNRPF Measured small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 4512.19 5655.52 1.25339
    Rooted 55.8956 63.9636 1.14434
    STT3A Squared oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 12326.4 16522.9 1.34045
    206 no value Measured atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 4577.5 1.24965
    Rooted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 140.508 122.878 1.14348
    DDOST Squared 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] 12326.4 16522.9 1.34045
    LUC7L Ranked luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 228.085 201.006 1.13472
    207 no value Measured splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 4771.21 5961.43 1.24946
    ATG3 Rooted apg3p; pc3-96 protein. [refseq;acc:nm_022488] 140.508 122.878 1.14348
    PSEN2 Ranked presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 285.684 252.234 1.13261
    SLC4A1AP Squared solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] 70525.9 52678.7 1.33879
    208 CACNG8 Measured voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 4068.78 5082.18 1.24907
    CKS2 Squared cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 70525.9 52678.7 1.33879
    DDX24 Rooted atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 46.901 53.624 1.14334
    SKP1A Ranked 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] 285.684 252.234 1.13261

    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/