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 Filtered Network Comparison Type Interaction Map green red network_comparison
    Results: HTML CSV LaTeX Showing element 2030 to 2079 of 3228 in total
    Value Type  : Ranked
    Filtered  : 1
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    		Hugo
    		description
    		green
    		red
    		network_comparison
    2030 GPT2 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] 191.677 189.999 1.00883
    2031 TTRAP traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] 216.562 218.466 1.00879
    2032 CAPZA3 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] 213.46 215.322 1.00872
    2033 CAPZB f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
    2034 CENTB5 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] 220.812 218.919 1.00865
    2035 CENTB2 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
    2036 LMNB1 lamin b1. [swissprot;acc:p20700] 220.813
    2037 CENTB1 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] 220.812
    2038 LMNA lamin a/c (70 kda lamin). [swissprot;acc:p02545] 220.811 218.92 1.00864
    2039 ACSS2 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 192.191 190.551 1.00861
    2040 T brachyury protein (t protein). [swissprot;acc:o15178] 208.803 210.586 1.00854
    2041 UBQLN4 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] 195.141 196.808
    2042 TBX19 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] 208.803 210.586
    2043 UBQLN1 ubiquilin 1 isoform 1. [refseq;acc:nm_013438] 195.173 196.837 1.00853
    2044 AP3B1 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 198.24 199.928 1.00851
    2045 C19orf29 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]
    2046 no value adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]
    2047 SLC2A6 solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] 226.003 224.124 1.00838
    2048 SLC2A8 solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]
    2049 EIF2B2 translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] 222.634 220.787 1.00837
    2050 SH3BGR sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] 216.981 218.79 1.00834
    2051 OXR1 oxidation resistance 1. [refseq;acc:nm_181354]
    2052 AZIN1 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] 205.95 207.667
    2053 LATS2 lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] 216.981 218.79
    2054 ADC ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] 205.948 207.665
    2055 DYM dymeclin. [refseq;acc:nm_017653] 216.981 218.79
    2056 SH3BGRL sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]
    2057 LATS1 lats homolog 1. [refseq;acc:nm_004690]
    2058 no value sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
    2059 NCOA7 nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]
    2060 C20orf118 dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]
    2061 TBC1D22B tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]
    2062 TBC1D22A tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]
    2063 ODC1 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] 205.923 207.638 1.00833
    2064 AASS aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 205.939 207.655
    2065 UBE2N 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] 212.561 214.328 1.00831
    2066 PCNA proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] 231.001 229.102 1.00829
    2067 ADSL adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 191.639 193.226 1.00828
    2068 FAIM fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] 222.61 220.8 1.0082
    2069 MAP2K1 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] 215.807 217.555 1.0081
    2070 RACGAP1 rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] 225.008 223.199
    2071 KSR1 similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] 215.807 217.555
    2072 MAP2K2 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]
    2073 PAPD5 topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] 227.433 229.267 1.00806
    2074 POLG dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 214.599 216.324 1.00804
    2075 CD109 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] 223.483 221.703 1.00803
    2076 PIN1 peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526]
    2077 IRX4 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]
    2078 FIGNL1 fidgetin-like 1. [refseq;acc:nm_022116] 213.814 215.511 1.00794
    2079 PIK3C2G 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] 214.28 215.967 1.00787

    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/