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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
green
red
network_comparison
801 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Squared Subtracted 24595.9 20613.1 3982.8
802 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 1390.33 779.167 611.163
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 23960.7 19987.6 3973.1
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 23416.5 20131.3 1.16319
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Ranked Subtracted 221.785 212.386 9.399
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Measured Divided 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
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 86.2754 82.1841 4.0913
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 Divided 26254.5 22573.3 1.16308
calsyntenin-1 precursor. [swissprot;acc:o94985] Rooted Subtracted 86.2754 82.1841 4.0913
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 1390.33 779.167 611.163
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 7167.96 6455.02 1.11045
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 221.785 212.386 1.04425
syntaxin 1b. [swissprot;acc:q15531] Subtracted 9.399
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 Divided 51.3516 54.6759 1.06474
transforming protein rhoc (h9). [swissprot;acc:p08134] Squared Subtracted 23960.7 19987.6 3973.1
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] Rooted Divided 79.1931 74.3877 1.0646
a kindred of iglon. [refseq;acc:nm_173808] Ranked 221.785 212.386 1.04425
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Subtracted 9.399
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Measured Divided 7517.97 6770.78 1.11036
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 1390.33 779.167 611.163
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] Rooted 86.2754 82.1841 4.0913
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Squared 23960.7 19987.6 3973.1
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Divided 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
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Squared Subtracted 23960.7 19987.6 3973.1
60s ribosomal protein l39. [swissprot;acc:p02404] Measured Divided 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
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared 17890 15384.8 1.16284
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Ranked Subtracted 221.785 212.386 9.399
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 1390.33 779.167 611.163
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Rooted 86.2753 82.184 4.0913
806 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 58.6426 62.4161 1.06435
60s ribosomal protein l18a. [swissprot;acc:q02543] Measured 5226.71 4708.61 1.11003
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked 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
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Ranked Subtracted 276.773 267.447 9.326
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 1390.33 779.167 611.163
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Rooted 86.2753 82.184 4.0913
transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 23960.7 19987.6 3973.1
807 40s ribosomal protein s19. [swissprot;acc:p39019] Measured Divided 5226.71 4708.61 1.11003
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted 1390.33 779.167 611.163
gk001 protein. [refseq;acc:nm_020198] Rooted 86.2753 82.184 4.0913
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 Divided 29720.6 25560.1 1.16277
mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 21214 17248.4 3965.6
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Rooted Divided 58.6426 62.416 1.06435
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Ranked 221.785 212.386 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 227.796 218.521 9.275
808 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 213.912 223.186 9.274

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/