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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1780 to 1829 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1780 germ cell-less. [refseq;acc:nm_022471] no value 206.335 203.877 1.01206
    1781 pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] PBX3 206.332 203.874
    1782 hyporthetical protein mgc27169. [refseq;acc:nm_176782] C1orf179
    1783 homeobox protein meis1. [swissprot;acc:o00470] MEIS1
    1784 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] MEIS2
    1785 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] BAG2
    1786 pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] no value
    1787 pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] PBX4
    1788 homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] MEIS3
    1789 ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] RNASEH2A 210.997 213.539 1.01205
    1790 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] no value 203.759 201.349 1.01197
    1791 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 217.866 215.295 1.01194
    1792 elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] ELAVL4 217.766 215.199 1.01193
    1793 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] NME2P1 193.1 190.823
    1794 nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] no value 193.138 190.861
    1795 elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] ELAVL2 217.724 215.158
    1796 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] TOP2B 203.759 201.357
    1797 nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] NME2 193.111 190.834
    1798 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] ELAVL1 217.807 215.242 1.01192
    1799 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] ACTN2 217.016 214.481 1.01182
    1800 dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] DYRK1A 217.011 1.0118
    1801 cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] CUGBP1 217.984 215.441
    1802 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] ELP4 217.011 214.481
    1803 dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] DYRK1B
    1804 cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561] CUGBP2 217.984 215.442
    1805 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] ACTN4 217.008 214.482 1.01178
    1806 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] ACTN1 217.009
    1807 ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] RALGPS1 211.102 208.651 1.01175
    1808 ral-a exchange factor ralgps2. [refseq;acc:nm_152663] RALGPS2
    1809 stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] STUB1
    1810 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] no value 223.214 225.827 1.01171
    1811 polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] GALNT2 216.854 214.35 1.01168
    1812 cyclin c. [swissprot;acc:p24863] CCNC 217.071 214.564
    1813 similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] GALNTL1 216.854 214.35
    1814 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] PPP1CC 122.3 123.727 1.01167
    1815 dpy-30-like protein. [swissprot;acc:q9c005] no value 220.462 217.926 1.01164
    1816 rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] RAB11FIP1
    1817 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] RAB11FIP5
    1818 neighbor of cox4. [swissprot;acc:o43402] COX4NB
    1819 protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] C14orf122
    1820 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] ATP9A
    1821 rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] RBM38 218.36 215.874 1.01152
    1822 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] PFKL 240.32 243.085 1.01151
    1823 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] FXR2 202.386 200.086 1.0115
    1824 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] CAPZA1 214.722 212.281
    1825 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] FXR1 202.386 200.086
    1826 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] NUP43 202.393 200.094 1.01149
    1827 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] NME3 191.39 189.219 1.01147
    1828 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] FMR1 202.41 200.115
    1829 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] CAD 212.884 215.323 1.01146

    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/