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 Value Type red Network Comparison Type Interaction Map Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
Network Comparison Type
network_comparison
green
801 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Squared 20613.1 Subtracted 3982.8 24595.9
802 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 779.167 611.163 1390.33
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 19987.6 3973.1 23960.7
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 20131.3 Divided 1.16319 23416.5
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Ranked 212.386 Subtracted 9.399 221.785
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Measured 6455.66 Divided 1.11047 7168.82
testis-specific protein tex28. [swissprot;acc:o15482] Ranked 212.386 1.04425 221.785
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 54.6759 1.06474 51.3516
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 82.1841 Subtracted 4.0913 86.2754
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 22573.3 Divided 1.16308 26254.5
calsyntenin-1 precursor. [swissprot;acc:o94985] Rooted 82.1841 Subtracted 4.0913 86.2754
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 779.167 611.163 1390.33
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 6455.02 Divided 1.11045 7167.96
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 212.386 1.04425 221.785
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 54.6759 Divided 1.06474 51.3516
transforming protein rhoc (h9). [swissprot;acc:p08134] Squared 19987.6 Subtracted 3973.1 23960.7
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 74.3877 Divided 1.0646 79.1931
a kindred of iglon. [refseq;acc:nm_173808] Ranked 212.386 1.04425 221.785
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 6770.78 Divided 1.11036 7517.97
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 779.167 Subtracted 611.163 1390.33
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 82.1841 4.0913 86.2754
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Squared 19987.6 3973.1 23960.7
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 24954.5 Divided 1.16302 29022.6
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 74.3557 1.0645 79.1513
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Squared 19987.6 Subtracted 3973.1 23960.7
60s ribosomal protein l39. [swissprot;acc:p02404] Measured 4708.61 Divided 1.11003 5226.71
ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Ranked 212.386 1.04425 221.785
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared 15384.8 1.16284 17890
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Ranked 212.386 Subtracted 9.399 221.785
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 779.167 611.163 1390.33
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Rooted 82.184 4.0913 86.2753
806 40s ribosomal protein s26. [swissprot;acc:p02383] 62.4161 Divided 1.06435 58.6426
60s ribosomal protein l18a. [swissprot;acc:q02543] Measured 4708.61 1.11003 5226.71
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked 212.386 1.04425 221.785
inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Squared 25555.4 1.16278 29715.4
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Ranked 267.447 Subtracted 9.326 276.773
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 611.163 1390.33
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Rooted 82.184 4.0913 86.2753
transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 19987.6 3973.1 23960.7
807 40s ribosomal protein s19. [swissprot;acc:p39019] Measured 4708.61 Divided 1.11003 5226.71
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 779.167 Subtracted 611.163 1390.33
gk001 protein. [refseq;acc:nm_020198] Rooted 82.184 4.0913 86.2753
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 25560.1 Divided 1.16277 29720.6
mad protein (max dimerizer). [swissprot;acc:q05195] 17248.4 Subtracted 3965.6 21214
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Rooted 62.416 Divided 1.06435 58.6426
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Ranked 212.386 1.04425 221.785
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] 218.521 Subtracted 9.275 227.796
808 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 9.274 213.912

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/