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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1901 to 1950 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
951 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] High confidence 5364.3 5885.48 1.09716
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Low confidence 8212.76 8531.84 1.03885
952 ptpl1-associated rhogap 1. [refseq;acc:nm_004815] 8628.48 8963.68
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] High confidence 5364.3 5885.48 1.09716
953 casein kinase i alpha s-like. [refseq;acc:nm_145203] 4906.33 5382.5 1.09705
glyoxylate reductase/hydroxypyruvate reductase. [refseq;acc:nm_012203] Low confidence 8582.43 8915.89 1.03885
954 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] 8212.76 8531.84
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] High confidence 4906.33 5382.5 1.09705
955 camp responsive element binding protein 3; luman; cyclic amp response element (cre)-binding protein/activating transcription factor 1; basic leucine zipper protein; transcription factor lzip-alpha. [refseq;acc:nm_006368] Low confidence 8212.76 8531.84 1.03885
uridine kinase-like 1. [swissprot;acc:q9nwz5] High confidence 5548.78 6086.89 1.09698
956 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 5364.77 5884.89 1.09695
myeloblast kiaa0223 (fragment). [sptrembl;acc:q92619] Low confidence 8628.43 8963.59 1.03884
957 nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] 7895.83 8202.18 1.0388
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] High confidence 4483.26 4917.77 1.09692
958 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Low confidence 8059.35 8371.9 1.03878
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] High confidence 4483.26 4917.77 1.09692
959 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Low confidence 8059.5 8371.83 1.03875
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] High confidence 4379.28 4803.59 1.09689
960 protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] 11773 10733.2 1.09688
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Low confidence 8206.42 8524.26 1.03873
961 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 8484.77 8813.34 1.03872
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] High confidence 11773 10733.2 1.09688
962 e-1 enzyme. [refseq;acc:nm_021204] Low confidence 8312.5 8634.21 1.0387
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] High confidence 11773 10733.2 1.09688
963 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073]
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Low confidence 8248.55 8567.81 1.0387
964 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] High confidence 11773 10733.2 1.09688
renin precursor, renal (ec 3.4.23.15) (angiotensinogenase). [swissprot;acc:p00797] Low confidence 8526.66 8856.56 1.03869
965 aspartyl protease 3 (fragment). [sptrembl;acc:q9uhb3] 8526.39 8856.19 1.03868
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] High confidence 11773.7 10733.8 1.09688
966 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 7817.9 8575.12 1.09686
ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [refseq;acc:nm_007322] Low confidence 8277.48 8597.67 1.03868
967 napsin 1 precursor (ec 3.4.23.-) (napsin a) (napa) (ta01/ta02) (aspartyl protease 4) (asp 4) (asp4). [swissprot;acc:o96009] 8526.26 8856.01 1.03867
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] High confidence 7813.35 8569.96 1.09684
968 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Low confidence 7882.49 8187.15 1.03865
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] High confidence 7813.48 8570.11 1.09684
969 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 7813.34 8569.95
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Low confidence 7935.62 8242.19 1.03863
970 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] High confidence 7813.45 8570.07 1.09684
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Low confidence 8269.17 8588.13 1.03857
971 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] High confidence 7813.36 8569.97 1.09684
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Low confidence 7462.66 7750 1.0385
972 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] High confidence 7813.48 8570.11 1.09684
wd-repeat containing protein ciao 1. [swissprot;acc:o76071] Low confidence 8307.14 8626.88 1.03849
973 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] High confidence 7810.11 8566.29 1.09682
nad(p)-dependent steroid dehydrogenase (ec 1.1.1.-) (h105e3 protein). [swissprot;acc:q15738] Low confidence 8163.8 8477.59 1.03844
974 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] High confidence 5365.06 5884.52 1.09682
protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [swissprot;acc:q06124] Low confidence 8375.25 8696.93 1.03841
975 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] High confidence 5365.14 5884.43 1.09679
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Low confidence 7940.02 8244.95 1.0384

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/