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 2051 to 2100 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2051 oxidation resistance 1. [refseq;acc:nm_181354] OXR1 218.79 216.981 1.00834
    2052 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] AZIN1 207.667 205.95
    2053 lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] LATS2 218.79 216.981
    2054 ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] ADC 207.665 205.948
    2055 dymeclin. [refseq;acc:nm_017653] DYM 218.79 216.981
    2056 sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] SH3BGRL
    2057 lats homolog 1. [refseq;acc:nm_004690] LATS1
    2058 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] no value
    2059 nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] NCOA7
    2060 dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125] C20orf118
    2061 tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19] TBC1D22B
    2062 tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7] TBC1D22A
    2063 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] ODC1 207.638 205.923 1.00833
    2064 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] AASS 207.655 205.939
    2065 ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] UBE2N 214.328 212.561 1.00831
    2066 proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] PCNA 229.102 231.001 1.00829
    2067 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] ADSL 193.226 191.639 1.00828
    2068 fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] FAIM 220.8 222.61 1.0082
    2069 dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] MAP2K1 217.555 215.807 1.0081
    2070 rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] RACGAP1 223.199 225.008
    2071 similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] KSR1 217.555 215.807
    2072 dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] MAP2K2
    2073 topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] PAPD5 229.267 227.433 1.00806
    2074 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] POLG 216.324 214.599 1.00804
    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

    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/