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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
green
red
network_comparison
801 zinc finger protein gli3. [swissprot;acc:p10071] Squared Low confidence 44591.2 46876.8 1.05126
802 dc12 protein. [refseq;acc:nm_020187] Ranked 198.117 203.345 1.02639
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Measured 8162.73 7837.99 1.04143
lysine-deficient protein kinase 2; mitogen-activated protein kinase kinase kinase; serologically defined colon cancer antigen 43. [refseq;acc:nm_006648] Rooted 73.4673 70.5871 1.0408
n27c7-4 protein. [sptrembl;acc:q8wyq3] Squared 45758.6 48101.4 1.0512
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] High confidence 23416.5 20131.3 1.16319
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Measured 7168.82 6455.66 1.11047
testis-specific protein tex28. [swissprot;acc:o15482] Ranked 221.785 212.386 1.04425
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Rooted 51.3516 54.6759 1.06474
803 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Squared 26254.5 22573.3 1.16308
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kda subunit precursor (ec 2.4.1.119) (ribophorin i) (rpn-i). [swissprot;acc:p04843] Ranked Low confidence 194.441 199.573 1.02639
glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] Squared 44335 46605.1 1.0512
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Measured High confidence 7167.96 6455.02 1.11045
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Low confidence 8162.73 7837.99 1.04143
protein kinase, lysine deficient 4; putative protein kinase wnk4. [refseq;acc:nm_032387] Rooted 73.4673 70.5871 1.0408
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked High confidence 221.785 212.386 1.04425
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Rooted 51.3516 54.6759 1.06474
804 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 79.1931 74.3877 1.0646
a kindred of iglon. [refseq;acc:nm_173808] Ranked 221.785 212.386 1.04425
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Low confidence 199.267 204.519 1.02636
glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] Squared 44335 46605.1 1.0512
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Measured High confidence 7517.97 6770.78 1.11036
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Rooted Low confidence 73.4673 70.5871 1.0408
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Measured 8162.73 7837.99 1.04143
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Squared High confidence 29022.6 24954.5 1.16302
805 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Rooted 79.1513 74.3557 1.0645
60s ribosomal protein l39. [swissprot;acc:p02404] Measured 5226.71 4708.61 1.11003
ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Ranked 221.785 212.386 1.04425
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Rooted Low confidence 74.9692 72.0306 1.0408
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared High confidence 17890 15384.8 1.16284
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Measured Low confidence 8162.73 7837.99 1.04143
sorting nexin 16. [swissprot;acc:p57768] Squared 41772.3 43910.5 1.05119
synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Ranked 193.399 198.496 1.02635
806 40s ribosomal protein s26. [swissprot;acc:p02383] Rooted High confidence 58.6426 62.4161 1.06435
60s ribosomal protein l18a. [swissprot;acc:q02543] Measured 5226.71 4708.61 1.11003
glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Squared Low confidence 45485.5 47813.4 1.05118
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked High confidence 221.785 212.386 1.04425
inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Squared 29715.4 25555.4 1.16278
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Measured Low confidence 8726.61 8379.95 1.04137
protein kinase, lysine deficient 1; kinase deficient protein. [refseq;acc:nm_018979] Rooted 73.4673 70.5871 1.0408
vacuolar atp synthase subunit c (ec 3.6.3.14) (v-atpase c subunit) (vacuolar proton pump c subunit). [swissprot;acc:p21283] Ranked 197.173 202.369 1.02635
807 40s ribosomal protein s19. [swissprot;acc:p39019] Measured High confidence 5226.71 4708.61 1.11003
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Low confidence 8614.36 8272.57 1.04132
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 44873.3 47169.4 1.05117
exonuclease nef-sp. [refseq;acc:nm_030941] Rooted 73.4673 70.5871 1.0408
inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Squared High confidence 29720.6 25560.1 1.16277
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Rooted 58.6426 62.416 1.06435
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Ranked Low confidence 195.631 200.782 1.02633
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] High confidence 221.785 212.386 1.04425
808 60s ribosomal protein l31. [swissprot;acc:p12947] Measured 5226.71 4708.61 1.11003

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/