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 2075 to 2124 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2075 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] CD109 221.703 223.483 1.00803
    2076 peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] PIN1
    2077 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] IRX4
    2078 fidgetin-like 1. [refseq;acc:nm_022116] FIGNL1 215.511 213.814 1.00794
    2079 phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] PIK3C2G 215.967 214.28 1.00787
    2080 phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] PIK3C2B
    2081 dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] DNM1L
    2082 phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] PIK3C2A
    2083 vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] PTPRA 215.258 213.579 1.00786
    2084 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] no value 222.548 224.293 1.00784
    2085 isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213] IDH3A 222.58 224.32 1.00782
    2086 isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837] IDH3B
    2087 isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553] IDH3G
    2088 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] MPP3 218.124 216.433 1.00781
    2089 serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] UTP14A 215.144 213.479 1.0078
    2090 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] GFPT2 222.609 224.344 1.00779
    2091 rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] SNUPN 211.679 210.052 1.00775
    2092 evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] ECSIT 211.992 210.369 1.00772
    2093 ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] RBKS 209.994 208.387 1.00771
    2094 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] PMS2 207.321 205.747 1.00765
    2095 polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] POLS 229.266 227.53 1.00763
    2096 limkain beta 2. [refseq;acc:nm_025140] CCDC92 217.723 216.089 1.00756
    2097 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] CCDC85B 214.979 213.39 1.00745
    2098 ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] no value 177.515 178.831 1.00741
    2099 ubiquitin-like protein smt3a. [swissprot;acc:p55854] SUMO3 211.71 213.27 1.00737
    2100 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] no value
    2101 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] ACRC
    2102 eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] EIF5AP1 208.727 210.263 1.00736
    2103 transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] TKT 214.666 216.236 1.00731
    2104 thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] DTYMK 209.328 207.813 1.00729
    2105 eif-5a2 protein. [refseq;acc:nm_020390] EIF5A2 208.591 210.111
    2106 insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663] ISL1 197.489 196.061 1.00728
    2107 lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] LMO7 216.23 217.801 1.00727
    2108 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] ASL 216.36 217.93 1.00726
    2109 ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] RANBP2 219.032 217.47 1.00718
    2110 conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] COG6 211.099 209.607 1.00712
    2111 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] no value 219.047 217.511 1.00706
    2112 dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] POLR3K 223.415 224.989 1.00705
    2113 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] no value 219.055 217.533 1.007
    2114 triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] LIPF 214.632 213.14
    2115 ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] LIPM
    2116 lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] LIPA
    2117 seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] SARS2
    2118 seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] SARS
    2119 potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] KCMF1 221.248 222.788 1.00696
    2120 solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7] SLC23A1
    2121 heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991] HNRPA3
    2122 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] LGALS9 206.473 207.911
    2123 adp-ribosylation factor 4. [swissprot;acc:p18085] ARF4 221.248 222.788
    2124 fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] AKTIP

    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/