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 12814 to 12863 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1100 phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Squared Divided 25180.2 28821.7 1.14462
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Measured 6133.83 6690.18 1.0907
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Ranked Subtracted 218.484 212.675 5.809
1101 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Squared Divided 26583.7 30425.2 1.14451
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Rooted 61.5152 64.5623 1.04953
d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] Measured 6133.83 6690.18 1.0907
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Subtracted 6721.25 7238.34 517.09
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Ranked 218.484 212.675 5.809
heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Rooted 58.0289 61.136 3.1071
lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Ranked Divided 220.291 226.584 1.02857
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Squared Subtracted 26893.1 30139.8 3246.7
1102 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Ranked Divided 229.442 235.974 1.02847
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Subtracted 218.484 212.675 5.809
esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Squared Divided 26583.7 30425.2 1.14451
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Rooted 61.5152 64.5623 1.04953
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Measured 5462.88 5958.12 1.09066
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Rooted Subtracted 58.0289 61.136 3.1071
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Squared 26893.1 30139.8 3246.7
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Measured 7433.73 7950.61 516.88
1103 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Rooted Divided 61.5152 64.5623 1.04953
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Ranked Subtracted 218.484 212.675 5.809
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Measured Divided 5358.18 5843.73 1.09062
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Squared 19147.7 21914.4 1.14449
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Subtracted 23379.3 26625.2 3245.9
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Ranked Divided 229.441 235.972 1.02846
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Measured Subtracted 7433.73 7950.61 516.88
uridine kinase-like 1. [swissprot;acc:q9nwz5] Rooted 61.1919 64.2955 3.1036
1104 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Divided 61.5152 64.5623 1.04953
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Squared 24175.6 27657.3 1.14402
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] Ranked 231.922 238.486 1.0283
kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Measured 5359.72 5844.97 1.09054
mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] Squared Subtracted 28609.1 31855 3245.9
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Rooted 80.6874 83.7879 3.1005
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Measured 7433.73 7950.61 516.88
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Ranked 218.484 212.675 5.809
1105 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Divided 191.139 185.882 1.02828
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] Measured Subtracted 7433.73 7950.61 516.88
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Rooted Divided 61.5152 64.5623 1.04953
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Squared 24175.6 27657.3 1.14402
pxr2b protein. [refseq;acc:nm_016559] Rooted Subtracted 66.7327 69.832 3.0993
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Ranked 218.484 212.675 5.809
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Squared 20322.5 23567.1 3244.6
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Measured Divided 5460.49 5954.62 1.09049
1106 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Rooted 61.5152 64.5623 1.04953
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Subtracted 55.2209 52.1262 3.0947
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Squared Divided 24175.6 27657.3 1.14402
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Measured Subtracted 7433.73 7950.61 516.88
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Divided 5489.99 5986.63 1.09046
pxr2b protein. [refseq;acc:nm_016559] Ranked 212.945 207.109 1.02818
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Squared Subtracted 28606.2 31850.3 3244.1

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
- 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/