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 description Network Comparison Type Value Type Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
green
network_comparison
red
801 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Subtracted Squared 24595.9 3982.8 20613.1
802 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 1390.33 611.163 779.167
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 23960.7 3973.1 19987.6
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 23416.5 1.16319 20131.3
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Subtracted Ranked 221.785 9.399 212.386
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Divided Measured 7168.82 1.11047 6455.66
testis-specific protein tex28. [swissprot;acc:o15482] Ranked 221.785 1.04425 212.386
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 1.06474 54.6759
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 86.2754 4.0913 82.1841
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] Divided Squared 26254.5 1.16308 22573.3
calsyntenin-1 precursor. [swissprot;acc:o94985] Subtracted Rooted 86.2754 4.0913 82.1841
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 1390.33 611.163 779.167
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 7167.96 1.11045 6455.02
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 221.785 1.04425 212.386
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] Divided Rooted 51.3516 1.06474 54.6759
transforming protein rhoc (h9). [swissprot;acc:p08134] Subtracted Squared 23960.7 3973.1 19987.6
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] Divided Rooted 79.1931 1.0646 74.3877
a kindred of iglon. [refseq;acc:nm_173808] Ranked 221.785 1.04425 212.386
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] Divided Measured 7517.97 1.11036 6770.78
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 1390.33 611.163 779.167
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 4.0913 82.1841
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Squared 23960.7 3973.1 19987.6
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Divided 29022.6 1.16302 24954.5
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 1.0645 74.3557
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Subtracted Squared 23960.7 3973.1 19987.6
60s ribosomal protein l39. [swissprot;acc:p02404] Divided Measured 5226.71 1.11003 4708.61
ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Ranked 221.785 1.04425 212.386
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared 17890 1.16284 15384.8
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Subtracted Ranked 221.785 9.399 212.386
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 1390.33 611.163 779.167
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Rooted 86.2753 4.0913 82.184
806 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 58.6426 1.06435 62.4161
60s ribosomal protein l18a. [swissprot;acc:q02543] Measured 5226.71 1.11003 4708.61
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked 221.785 1.04425 212.386
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 1.16278 25555.4
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Subtracted Ranked 276.773 9.326 267.447
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 1390.33 611.163 779.167
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Rooted 86.2753 4.0913 82.184
transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 23960.7 3973.1 19987.6
807 40s ribosomal protein s19. [swissprot;acc:p39019] Divided Measured 5226.71 1.11003 4708.61
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted 1390.33 611.163 779.167
gk001 protein. [refseq;acc:nm_020198] Rooted 86.2753 4.0913 82.184
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 Squared 29720.6 1.16277 25560.1
mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 21214 3965.6 17248.4
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided Rooted 58.6426 1.06435 62.416
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Ranked 221.785 1.04425 212.386
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 9.275 218.521
808 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 213.912 9.274 223.186

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/