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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Network Comparison Type Value Type Gene description Rank green network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 2980 to 3029 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
green
network_comparison
red
tubulin-tyrosine ligase. [refseq;acc:nm_153712] 1853 215.564 1.01095 217.924
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 421 205.9 1.08403 223.202
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] 1980 207.529 1.00969 209.539
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] 1979
tumor differentially expressed protein 2. [refseq;acc:nm_178865] 1978
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] 2472 217.564 1.00301 218.218
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] 1203 213.606 1.02536 219.023
tumor protein d52 (n8 protein). [swissprot;acc:p55327] 1223 211.926 1.02493 206.771
tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] 1222 211.936 1.02496 206.774
tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] 1301 211.757 1.02371 206.852
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 2295 163.712 1.00523 162.86
tumor susceptibility gene 101 protein. [swissprot;acc:q99816] 2202 194.7 1.00652 195.97
twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] 2182 216.624 1.00664 218.062
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 1953 127.146 1.0098 125.912
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] 1033 214.406 1.03161 221.183
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 1019 214.409 1.03215 221.302
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 1562 170.455 1.01651 167.687
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 548 194.346 1.06645 207.26
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 656 204.622 1.05807 216.504
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 550 194.346 1.06645 207.26
tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925] 2858 0.00001 1 0.00001
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] 711 245.048 1.05411 232.468
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 190 198.444 1.14179 226.582
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 453 207.972 1.07784 224.161
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 751 212.875 1.04974 223.463
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 2002 216.769 1.00928 214.775
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 1199 235.508 1.02543 241.496
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] 821 231.453 1.0441 221.676
u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] 873 233.272 1.03948 224.413
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 764 211.707 1.04901 222.082
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 845 219.399 1.04193 228.599
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 589 214.546 1.06371 228.215
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 677 216.745 1.05628 228.944
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 430 210.888 1.07995 227.748
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 530 212.994 1.06803 227.483
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 650 216.276 1.05877 228.986
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 516 213.422 1.0695 228.255
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 910 209.207 1.03805 217.168
ubiquilin 1 isoform 1. [refseq;acc:nm_013438] 2043 195.173 1.00853 196.837
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] 457 226.578 1.07779 210.225
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 1302 212.584 1.02371 217.624
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 412 261.416 1.08567 240.788
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] 2197 195.064 1.00659 193.787
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 106 202.004 1.24913 252.329
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 558 144.041 1.06628 135.087
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 1 0.00001
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] 1380 213.876 1.02148 218.47
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 219.434 1.00402 218.555
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] 2230 219.336 1.00634 217.955

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/