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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1625 to 1674 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    204 no value Measured small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 4512.19 1.25339 5655.52
    Rooted 55.8956 1.14434 63.9636
    CPN2 Measured carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792] Low confidence 10374.8 1.07261 9672.48
    GNG8 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 211.484 1.05065 222.196
    LEO1 Rooted senescence downregulated leo1-like. [refseq;acc:nm_138792] 66.3503 1.06066 70.3749
    SSBP3 Squared single-stranded dna-binding protein 3 (sequence-specific single- stranded-dna-binding protein). [swissprot;acc:q9bww4] 52164.7 1.10763 47095.6
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] High confidence 12326.4 1.34045 16522.9
    TRPC5 Ranked short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 201.515 1.13516 228.752
    205 GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Low confidence 211.475 1.05061 222.177
    GP5 Measured platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] 10374.8 1.07261 9672.51
    LUC7L2 Ranked luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] High confidence 228.1 1.13501 200.968
    SLC9A7 Rooted solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [refseq;acc:nm_032591] Low confidence 66.3503 1.06066 70.3749
    SNRPF Measured small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] High confidence 4512.19 1.25339 5655.52
    Rooted 55.8956 1.14434 63.9636
    SSBP2 Squared single-stranded dna-binding protein 2 (sequence-specific single- stranded-dna-binding protein 2). [swissprot;acc:p81877] Low confidence 52164.4 1.10763 47095.3
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 12326.4 1.34045 16522.9
    206 no value Measured atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 1.24965 4577.5
    Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Low confidence 211.457 1.05051 222.138
    Rooted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] High confidence 140.508 1.14348 122.878
    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 1.34045 16522.9
    LUC7L Ranked luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 228.085 1.13472 201.006
    SLC15A2 Measured oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Low confidence 7583.48 1.07247 8133.08
    SSBP4 Squared single-stranded dna-binding protein 4. [swissprot;acc:q9bwg4] 52164.3 1.10763 47095.3
    STT3A Rooted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 70.4583 1.06063 74.7299
    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] High confidence 4771.21 1.24946 5961.43
    ANAPC10 Ranked anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Low confidence 213.495 1.05044 203.244
    ASNS Measured asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 9818 1.07247 10529.5
    ATG3 Rooted apg3p; pc3-96 protein. [refseq;acc:nm_022488] High confidence 140.508 1.14348 122.878
    CTSL2 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Low confidence 67.6503 1.06058 71.7486
    PSEN2 Ranked presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] High confidence 285.684 1.13261 252.234
    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 1.33879 52678.7
    TNN tenascin n precursor (fragment). [sptrembl;acc:q9uqp3] Low confidence 52163.9 1.10763 47095
    208 no value Measured transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 6557.13 1.07188 7028.46
    CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] High confidence 4068.78 1.24907 5082.18
    CKS2 Squared cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 70525.9 1.33879 52678.7
    CTSL1 Rooted cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Low confidence 67.647 1.06046 71.7367
    DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] High confidence 46.901 1.14334 53.624
    FMO6P Ranked putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Low confidence 209.792 1.05023 199.758
    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 1.13261 252.234
    TNR Squared tenascin r (restrictin, janusin). [refseq;acc:nm_003285] Low confidence 52163.9 1.10763 47095
    209 BRAF Measured b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 10348.7 1.0717 9656.36
    CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] High confidence 4068.78 1.24907 5082.18
    CAPN2 Rooted 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] 46.8525 1.14257 53.5324
    CTNNAL1 Squared catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 70525.9 1.33879 52678.7
    FBXW7 Ranked 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] 285.684 1.13261 252.234
    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 1.05017 199.757
    HSPB6 Rooted heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] 65.7756 1.0603 69.742
    TNC Squared tenascin precursor (tn) (hexabrachion) (cytotactin) (neuronectin) (gmem) (ji) (miotendinous antigen) (glioma-associated-extracellular matrix antigen) (gp 150-225) (tenascin-c) (tn-c). [swissprot;acc:p24821] 52164.7 1.10763 47095.6
    210 CACNG2 Measured voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] High confidence 4068.82 1.24906 5082.21
    CAPN1 Rooted calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 46.8525 1.14256 53.5316

    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/