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 3051 to 3100 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    763 N6AMT1 Ranked putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 228.78 218.091 1.04901
    PFKM Measured 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 4250.54 4729.67 1.11272
    764 no value Squared sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 21186.4 24698.3 1.16576
    CBS Rooted cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 63.5181 67.7402 1.06647
    PFKL Measured 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 4250.18 4729.12 1.11269
    PRPF3 Ranked u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 222.082 211.707 1.04901
    765 HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 229.045 218.343
    POLS Measured polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] 4726.38 5258.95 1.11268
    RHOC Rooted transforming protein rhoc (h9). [swissprot;acc:p08134] 63.5181 67.7402 1.06647
    SREBF1 Squared sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] 21186.4 24698.3 1.16576
    766 ATP5C1 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 24509.4 28571.6 1.16574
    TMEM189 Measured ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 6691.93 7445.09 1.11255
    TRIOBP Ranked protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 213.804 224.226 1.04875
    TST Rooted thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 63.5181 67.7402 1.06647
    767 no value Ranked rho interacting protein 3. [refseq;acc:nm_015134] 213.803 224.224 1.04874
    ATP5O Squared atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] 24509.4 28571.6 1.16574
    MPST Rooted 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 63.5181 67.7402 1.06647
    UGP2 Measured utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 6691.21 7444.22 1.11254
    768 DNAJB4 Ranked dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 210.946 221.225 1.04873
    EIF5 Squared eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 12108.4 14114.6 1.16569
    RHOA Rooted transforming protein rhoa (h12). [swissprot;acc:p06749] 63.5181 67.7402 1.06647
    UBE2V2 Measured 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] 6690.44 7443.29 1.11253
    769 no value Rooted 60s ribosomal protein l39. [swissprot;acc:p02404] 55.6817 59.3786 1.06639
    ATP6V1F Measured 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] 5873.77 6532.44 1.11214
    NAGS Squared n-acetylglutamate synthase. [refseq;acc:nm_153006] 20943 24412.8 1.16568
    PERLD1 Ranked cab2. [refseq;acc:nm_033419] 210.946 221.225 1.04873
    770 no value Measured 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] 5874.74 6533.34 1.11211
    Rooted 60s ribosomal protein l18a. [swissprot;acc:q02543] 55.6817 59.3786 1.06639
    DNAJB5 Ranked dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] 210.946 221.225 1.04873
    FBLN2 Squared fibulin-2 precursor. [swissprot;acc:p98095] 45189.6 52666.2 1.16545
    771 API5 Measured apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 5874.74 6533.34 1.11211
    DNAJB1 Ranked 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] 210.946 221.225 1.04873
    QRSL1 Squared glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 24418 28453.7 1.16528
    RPS19 Rooted 40s ribosomal protein s19. [swissprot;acc:p39019] 55.6817 59.3786 1.06639
    772 ETF1 Ranked eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] 210.946 221.225 1.04873
    FAAH Squared fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] 24418 28453.7 1.16528
    RPL31 Rooted 60s ribosomal protein l31. [swissprot;acc:p12947] 55.6817 59.3786 1.06639
    SEC13 Measured sec13-related protein. [swissprot;acc:p55735] 5874.76 6533.36 1.11211
    773 ATP6V1G3 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] 5874.74 6533.34
    COTL1 Squared coactosin-like protein. [swissprot;acc:q14019] 24418 28453.7 1.16528
    PPP1CC Rooted serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 127.967 120.003 1.06637
    VPS52 Ranked suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] 210.946 221.225 1.04873
    774 DPM1 Rooted 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] 65.3248 69.648 1.06618
    MCFD2 Ranked multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 1.04854
    SEC31A Measured yeast sec31p homolog. [refseq;acc:nm_014933] 5874.76 6533.36 1.11211
    UNG Squared uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 24418 28453.7 1.16528
    775 no value Ranked histone deacetylase 2 (hd2). [swissprot;acc:q92769] 226.003 215.541 1.04854
    ATP6V1G1 Measured 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] 5874.74 6533.33 1.11211
    CLTC Rooted clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 62.2385 58.38 1.06609
    PET112L Squared 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] 24418 28453.7 1.16528

    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/