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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2901 to 2950 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    726 FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Ranked 244.495 232.419 1.05196
    MLH3 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Measured 6327.86 7064.13 1.11635
    SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490] Squared 25911.7 30282.1 1.16867
    TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Rooted 51.4482 55.0529 1.07006
    727 ATP6V1H vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Squared 25911.5 30281.9 1.16867
    NUAK1 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Ranked 208.873 219.71 1.05188
    RPL24 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Measured 7087.23 7911.25 1.11627
    SF3A3 splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Rooted 59.7414 63.909 1.06976
    728 ASNSD1 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Measured 6000.23 6696.89 1.11611
    ATP6V1B2 vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Squared 25911.8 30282.2 1.16866
    B3GNT1 n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] Ranked 208.874 219.708 1.05187
    SF3A1 splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Rooted 59.7414 63.909 1.06976
    729 no value huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Ranked 208.874 219.708 1.05187
    ATP6V1A vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Measured 6000.23 6696.89 1.11611
    ATP6V1B1 vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Squared 25910.8 30280.9 1.16866
    EXOC6 exocyst complex component sec15a. [swissprot;acc:q8tag9] Rooted 62.5069 66.8603 1.06965
    730 no value dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Squared 24644.9 28800.7 1.16863
    ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Measured 6000.23 6696.89 1.11611
    EXOC6B exocyst complex component sec15b. [swissprot;acc:q9y2d4] Rooted 62.5729 66.9286 1.06961
    TIMM10 mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] Ranked 208.874 219.708 1.05187
    731 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Rooted 98.2298 91.8648 1.06929
    methyltransferase like 2. [refseq;acc:nm_018396] Measured 13241.4 11864 1.1161
    FH fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Ranked 208.874 219.708 1.05187
    VCL vinculin (metavinculin). [swissprot;acc:p18206] Squared 27463 32090.3 1.16849
    732 ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] 26029.8 30414.4 1.16845
    DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Measured 13241.4 11864 1.1161
    POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Rooted 51.8444 48.4963 1.06904
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Ranked 124.434 118.318 1.05169
    733 ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 164 155.961 1.05154
    FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Measured 13241.4 11864 1.1161
    NOL6 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Rooted 52.0099 55.5904 1.06884
    TCIRG1 vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Squared 26029.1 30413.6 1.16845
    734 no value presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Ranked 232.601 244.534 1.0513
    ATP6V0A1 vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Squared 26032.5 30417.7 1.16845
    LOH12CR1 loh1cr12. [refseq;acc:nm_058169] Rooted 57.805 61.7803 1.06877
    PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Measured 13241.4 11864 1.1161
    735 ATP6V0A4 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Squared 26030.5 30415.2 1.16844
    ATP6V0C vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Measured 5768.32 6434.78 1.11554
    CSDE1 unr protein. [swissprot;acc:o75534] Rooted 57.805 61.7803 1.06877
    RANP1 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Ranked 232.601 244.534 1.0513
    736 no value presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
    OSGEPL1 putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Squared 22017.1 25721.9 1.16827
    SGCZ sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Measured 5768.32 6434.78 1.11554
    WDR3 wd-repeat protein 3. [swissprot;acc:q9unx4] Rooted 51.5438 55.0853 1.06871
    737 no value pnas-18. [sptrembl;acc:q9bzu3] 97.8205 91.5467 1.06853
    ACBD3 golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Measured 5768.32 6434.78 1.11554
    SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Ranked 125.526 119.402 1.05129
    TLE2 transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Squared 31479.4 36770.8 1.16809
    738 no value transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 31467.1 36752.2 1.16796
    SGCD delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Measured 5768.32 6434.78 1.11554

    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/