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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3008 to 3057 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] 873 PRPF4 224.413 233.272 1.03948
    u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 764 PRPF3 222.082 211.707 1.04901
    u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 845 LSM1 228.599 219.399 1.04193
    u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 589 no value 228.215 214.546 1.06371
    u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 677 LSM4 228.944 216.745 1.05628
    u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 430 LSM5 227.748 210.888 1.07995
    u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 530 LSM6 227.483 212.994 1.06803
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 650 no value 228.986 216.276 1.05877
    u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 516 LSM8 228.255 213.422 1.0695
    uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 910 no value 217.168 209.207 1.03805
    ubiquilin 1 isoform 1. [refseq;acc:nm_013438] 2043 UBQLN1 196.837 195.173 1.00853
    ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] 457 UQCRB 210.225 226.578 1.07779
    ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 1302 UQCRC1 217.624 212.584 1.02371
    ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 412 UQCRFSL1 240.788 261.416 1.08567
    ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] 2197 COQ6 193.787 195.064 1.00659
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 106 COQ7 252.329 202.004 1.24913
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 558 no value 135.087 144.041 1.06628
    ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [swissprot;acc:q92995] 3192 USP13 0.00001 0.00001 1
    ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974] 3075 USP5
    ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] 1380 USP8 218.47 213.876 1.02148
    ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] 2370 UCHL5 218.555 219.434 1.00402
    ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] 2230 UFD1L 217.955 219.336 1.00634
    ubiquitin protein ligase. [refseq;acc:nm_130466] 2902 UBE3B 0.00001 0.00001 1
    ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314] 2493 UBE1 194.527 195.08 1.00284
    ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] 2492 UBE1C
    ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] 2641 UBE2A 220.658 220.386 1.00123
    ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] 2640 UBE2B
    ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] 1225 UBE2E1 166.846 170.989 1.02483
    ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] 2357 UBE2G2 198.181 197.346 1.00423
    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] 2065 UBE2N 214.328 212.561 1.00831
    ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 1608 TMEM189 208.106 204.867 1.01581
    ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] 1610 UBE2V2 208.122 204.886 1.01579
    ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] 2314 UBE2D2 194.743 195.708 1.00496
    ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 2254 no value 193.065 194.22 1.00598
    ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 2828 0.00001 0.00001 1
    ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763] 3094 UBE2S
    ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] 1226 UBE2E4P 166.846 170.989 1.02483
    ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] 2292 UBL4A 200.158 201.213 1.00527
    ubiquitin-like protein nedd8. [swissprot;acc:q15843] 3001 NEDD8 0.00001 0.00001 1
    ubiquitin-like protein smt3a. [swissprot;acc:p55854] 2099 SUMO3 211.71 213.27 1.00737
    ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 2100 no value
    ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] 2298 SUMO1P3 215.239 216.339 1.00511
    ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] 2443 UBE2I 217.073 216.364 1.00328
    ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670] 2729 OTUB1 202.123 202.06 1.00031
    ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] 2681 OTUB2 203.592 203.787 1.00096
    ubiquitin. [swissprot;acc:p02248] 1148 no value 209.061 203.518 1.02724
    1190 UBB 209.6 204.372 1.02558
    2310 UBC 216.617 215.529 1.00505
    ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] 2333 TMOD3 229.258 230.294 1.00452
    udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798] 2810 UGT2A1 0.00001 0.00001 1

    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/