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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Gene Rank Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
801 Rooted protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Subtracted 65.0565 69.1533 4.0968
802 Measured chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 779.167 1390.33 611.163
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Divided 6455.66 7168.82 1.11047
Ranked synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Subtracted 212.386 221.785 9.399
testis-specific protein tex28. [swissprot;acc:o15482] Divided 1.04425
Squared cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Subtracted 19987.6 23960.7 3973.1
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 20131.3 23416.5 1.16319
Rooted 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] 54.6759 51.3516 1.06474
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 82.1841 86.2754 4.0913
803 Measured doc-1 related protein (doc-1r). [swissprot;acc:o75956] 779.167 1390.33 611.163
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 6455.02 7167.96 1.11045
Ranked similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] 212.386 221.785 1.04425
syntaxin 1b. [swissprot;acc:q15531] Subtracted 9.399
Squared 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] Divided 22573.3 26254.5 1.16308
transforming protein rhoc (h9). [swissprot;acc:p08134] Subtracted 19987.6 23960.7 3973.1
Rooted calsyntenin-1 precursor. [swissprot;acc:o94985] 82.1841 86.2754 4.0913
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Divided 54.6759 51.3516 1.06474
804 Measured nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 6770.78 7517.97 1.11036
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 779.167 1390.33 611.163
Ranked a kindred of iglon. [refseq;acc:nm_173808] Divided 212.386 221.785 1.04425
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Subtracted 9.399
Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 19987.6 23960.7 3973.1
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Divided 24954.5 29022.6 1.16302
Rooted 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] 74.3877 79.1931 1.0646
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted 82.1841 86.2754 4.0913
805 Measured 60s ribosomal protein l39. [swissprot;acc:p02404] Divided 4708.61 5226.71 1.11003
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Subtracted 779.167 1390.33 611.163
Ranked ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Divided 212.386 221.785 1.04425
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Subtracted 9.399
Squared 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 19987.6 23960.7 3973.1
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Divided 15384.8 17890 1.16284
Rooted 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] 74.3557 79.1513 1.0645
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Subtracted 82.184 86.2753 4.0913
806 Measured 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 4708.61 5226.71 1.11003
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Subtracted 779.167 1390.33 611.163
Ranked inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Divided 212.386 221.785 1.04425
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Subtracted 267.447 276.773 9.326
Squared inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Divided 25555.4 29715.4 1.16278
transforming protein rhoa (h12). [swissprot;acc:p06749] Subtracted 19987.6 23960.7 3973.1
Rooted 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 62.4161 58.6426 1.06435
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Subtracted 82.184 86.2753 4.0913
807 Measured 40s ribosomal protein s19. [swissprot;acc:p39019] Divided 4708.61 5226.71 1.11003
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted 779.167 1390.33 611.163
Ranked palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Divided 212.386 221.785 1.04425
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Subtracted 218.521 227.796 9.275
Squared 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] Divided 25560.1 29720.6 1.16277
mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 17248.4 21214 3965.6
Rooted gk001 protein. [refseq;acc:nm_020198] 82.184 86.2753 4.0913
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided 62.416 58.6426 1.06435
808 Measured 60s ribosomal protein l31. [swissprot;acc:p12947] 4708.61 5226.71 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/