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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3058 to 3107 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    765 polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] POLS Measured 4726.38 5258.95 1.11268
    sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] SREBF1 Squared 21186.4 24698.3 1.16576
    transforming protein rhoc (h9). [swissprot;acc:p08134] RHOC Rooted 63.5181 67.7402 1.06647
    766 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] ATP5C1 Squared 24509.4 28571.6 1.16574
    protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] TRIOBP Ranked 213.804 224.226 1.04875
    thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] TST Rooted 63.5181 67.7402 1.06647
    ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] TMEM189 Measured 6691.93 7445.09 1.11255
    767 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST Rooted 63.5181 67.7402 1.06647
    atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] ATP5O Squared 24509.4 28571.6 1.16574
    rho interacting protein 3. [refseq;acc:nm_015134] no value Ranked 213.803 224.224 1.04874
    utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] UGP2 Measured 6691.21 7444.22 1.11254
    768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] DNAJB4 Ranked 210.946 221.225 1.04873
    eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] EIF5 Squared 12108.4 14114.6 1.16569
    transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA Rooted 63.5181 67.7402 1.06647
    ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] UBE2V2 Measured 6690.44 7443.29 1.11253
    769 60s ribosomal protein l39. [swissprot;acc:p02404] no value Rooted 55.6817 59.3786 1.06639
    cab2. [refseq;acc:nm_033419] PERLD1 Ranked 210.946 221.225 1.04873
    n-acetylglutamate synthase. [refseq;acc:nm_153006] NAGS Squared 20943 24412.8 1.16568
    vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] ATP6V1F Measured 5873.77 6532.44 1.11214
    770 60s ribosomal protein l18a. [swissprot;acc:q02543] no value Rooted 55.6817 59.3786 1.06639
    dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] DNAJB5 Ranked 210.946 221.225 1.04873
    fibulin-2 precursor. [swissprot;acc:p98095] FBLN2 Squared 45189.6 52666.2 1.16545
    vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] no value Measured 5874.74 6533.34 1.11211
    771 40s ribosomal protein s19. [swissprot;acc:p39019] RPS19 Rooted 55.6817 59.3786 1.06639
    apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] API5 Measured 5874.74 6533.34 1.11211
    dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] DNAJB1 Ranked 210.946 221.225 1.04873
    glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] QRSL1 Squared 24418 28453.7 1.16528
    772 60s ribosomal protein l31. [swissprot;acc:p12947] RPL31 Rooted 55.6817 59.3786 1.06639
    eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] ETF1 Ranked 210.946 221.225 1.04873
    fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] FAAH Squared 24418 28453.7 1.16528
    sec13-related protein. [swissprot;acc:p55735] SEC13 Measured 5874.76 6533.36 1.11211
    773 coactosin-like protein. [swissprot;acc:q14019] COTL1 Squared 24418 28453.7 1.16528
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] PPP1CC Rooted 127.967 120.003 1.06637
    suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] VPS52 Ranked 210.946 221.225 1.04873
    vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] ATP6V1G3 Measured 5874.74 6533.34 1.11211
    774 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] DPM1 Rooted 65.3248 69.648 1.06618
    multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] MCFD2 Ranked 225.996 215.535 1.04854
    uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] UNG Squared 24418 28453.7 1.16528
    yeast sec31p homolog. [refseq;acc:nm_014933] SEC31A Measured 5874.76 6533.36 1.11211
    775 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] CLTC Rooted 62.2385 58.38 1.06609
    histone deacetylase 2 (hd2). [swissprot;acc:q92769] no value Ranked 226.003 215.541 1.04854
    probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] PET112L Squared 24418 28453.7 1.16528
    vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] ATP6V1G1 Measured 5874.74 6533.33 1.11211
    776 40s ribosomal protein s13. [swissprot;acc:q02546] RPS13 Squared 21976 25607.9 1.16527
    dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] no value Ranked 225.996 215.535 1.04854
    ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] GDAP1L1 Measured 5874.76 6533.36 1.11211
    sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] no value Rooted 59.6869 63.6262 1.066
    777 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] DDX39 Measured 5874.74 6533.34 1.11211
    histone deacetylase 1 (hd1). [swissprot;acc:q13547] HDAC1 Ranked 225.989 215.53 1.04853
    importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] KPNA3 Squared 33908.1 39510.9 1.16523

    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/