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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2012 to 2061 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2012 dead-box protein. [refseq;acc:nm_018665] DDX43 193.517 191.766 1.00913
    2013 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] PPP1R12B 217.662 215.693
    2014 protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] PPP1R12A 217.676 215.709 1.00912
    2015 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] TOP3A 217.941 215.979 1.00908
    2016 electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] ETFDH 199.092 197.301
    2017 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] RRS1 127.397 128.553 1.00907
    2018 serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] PPP1CA
    2019 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] no value 215.799 213.865 1.00904
    2020 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] KIAA0664 223.168 221.176 1.00901
    2021 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] COQ3 208.601 210.464 1.00893
    2022 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] ATP5S
    2023 guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] GDA
    2024 vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] VPS33B 215.553 213.663 1.00885
    2025 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] GPT 189.987 191.668
    2026 vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] VPS11 215.553 213.663
    2027 lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] LIN7C 225.015 223.041
    2028 vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] VPS33A 215.553 213.663
    2029 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] CCBL1 189.999 191.677 1.00883
    2030 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] GPT2
    2031 traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] TTRAP 218.466 216.562 1.00879
    2032 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] CAPZA3 215.322 213.46 1.00872
    2033 f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] CAPZB
    2034 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] CENTB5 218.919 220.812 1.00865
    2035 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] CENTB2
    2036 lamin b1. [swissprot;acc:p20700] LMNB1 220.813
    2037 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] CENTB1 220.812
    2038 lamin a/c (70 kda lamin). [swissprot;acc:p02545] LMNA 218.92 220.811 1.00864
    2039 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] ACSS2 190.551 192.191 1.00861
    2040 brachyury protein (t protein). [swissprot;acc:o15178] T 210.586 208.803 1.00854
    2041 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] UBQLN4 196.808 195.141
    2042 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] TBX19 210.586 208.803
    2043 ubiquilin 1 isoform 1. [refseq;acc:nm_013438] UBQLN1 196.837 195.173 1.00853
    2044 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] AP3B1 199.928 198.24 1.00851
    2045 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] C19orf29
    2046 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] no value
    2047 solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] SLC2A6 224.124 226.003 1.00838
    2048 solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] SLC2A8
    2049 translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] EIF2B2 220.787 222.634 1.00837
    2050 sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] SH3BGR 218.79 216.981 1.00834
    2051 oxidation resistance 1. [refseq;acc:nm_181354] OXR1
    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

    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/