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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3001 to 3050 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] 2606 4450.84 4517.54 1.01499
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 112 4366.44 5899.76 1.35116
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 300 4914.27 5907.12 1.20203
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 660 5575.18 6254.85 1.12191
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 1312 5675.96 6136.47 1.08113
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 977 4115.9 4513.14 1.09651
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] 2440 4730.66 4891.26 1.03395
u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] 2489 5637.59 5804.47 1.0296
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 521 5390.78 6142.07 1.13937
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 375 4700.42 5492.63 1.16854
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 298 4633.92 5572.85 1.20262
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 323 4620.76 5501.94 1.1907
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 237 4567.04 5631.2 1.23301
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 289 4682.88 5646.19 1.20571
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 312 4598.21 5500.48 1.19622
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 269 4590.18 5575.52 1.21466
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 854 6562.98 7242.37 1.10352
ubiquilin 1 isoform 1. [refseq;acc:nm_013438] 2644 9125.08 9217 1.01007
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] 1659 5488.7 5131.89 1.06953
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 434 5246.38 6037.37 1.15077
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 2539 3805.17 3718.86 1.02321
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] 2164 6952.66 7315.06 1.05212
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 244 4250.14 5211.25 1.22614
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 145 16771.5 12889.1 1.30122
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 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
ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] 2279 5783.73 6048.91 1.04585
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] 1885 5826 6195.48 1.06342
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] 1949 6230.21 6608.64 1.06074
ubiquitin protein ligase. [refseq;acc:nm_130466] 2902 0.00001 0.00001 1
ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314] 1912 6858.84 7287.27 1.06246
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] 1911
ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] 1436 5759.68 6203.63 1.07708
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] 1435
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] 1242 11143.5 10276.3 1.08439
ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] 2259 6486.84 6786.23 1.04615
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] 988 6229.69 6829.58 1.0963
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 766 6691.93 7445.09 1.11255
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] 768 6690.44 7443.29 1.11253
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] 2597 8104.84 7970.2 1.01689
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] 2545 8285.65 8107.49 1.02197
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
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] 1243 11143.5 10276.3 1.08439
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] 2526 8695.15 8912.98 1.02505
ubiquitin-like protein nedd8. [swissprot;acc:q15843] 3001 0.00001 0.00001 1
ubiquitin-like protein smt3a. [swissprot;acc:p55854] 1170 5826.34 6335.98 1.08747
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 1171 5826.29 6335.93
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] 1586 5784.36 6198.73 1.07164
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] 1454 5770.74 6210.65 1.07623

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
- 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/