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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 [...,...].
Rank Gene description Network Comparison Type Value 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
description
Network Comparison Type
Value Type
red
green
network_comparison
801 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Subtracted Squared 20613.1 24595.9 3982.8
802 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 779.167 1390.33 611.163
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 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
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Subtracted Ranked 212.386 221.785 9.399
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Divided Measured 6455.66 7168.82 1.11047
testis-specific protein tex28. [swissprot;acc:o15482] Ranked 212.386 221.785 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 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 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 22573.3 26254.5 1.16308
calsyntenin-1 precursor. [swissprot;acc:o94985] Subtracted Rooted 82.1841 86.2754 4.0913
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 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
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 212.386 221.785 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] Divided Rooted 54.6759 51.3516 1.06474
transforming protein rhoc (h9). [swissprot;acc:p08134] Subtracted Squared 19987.6 23960.7 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] Divided Rooted 74.3877 79.1931 1.0646
a kindred of iglon. [refseq;acc:nm_173808] Ranked 212.386 221.785 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] Divided Measured 6770.78 7517.97 1.11036
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 779.167 1390.33 611.163
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 82.1841 86.2754 4.0913
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Squared 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
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 79.1513 1.0645
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Subtracted Squared 19987.6 23960.7 3973.1
60s ribosomal protein l39. [swissprot;acc:p02404] Divided Measured 4708.61 5226.71 1.11003
ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Ranked 212.386 221.785 1.04425
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared 15384.8 17890 1.16284
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Subtracted Ranked 212.386 221.785 9.399
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 779.167 1390.33 611.163
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Rooted 82.184 86.2753 4.0913
806 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 62.4161 58.6426 1.06435
60s ribosomal protein l18a. [swissprot;acc:q02543] Measured 4708.61 5226.71 1.11003
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked 212.386 221.785 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 25555.4 29715.4 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] Subtracted Ranked 267.447 276.773 9.326
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 611.163
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Rooted 82.184 86.2753 4.0913
transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 19987.6 23960.7 3973.1
807 40s ribosomal protein s19. [swissprot;acc:p39019] Divided Measured 4708.61 5226.71 1.11003
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted 779.167 1390.33 611.163
gk001 protein. [refseq;acc:nm_020198] Rooted 82.184 86.2753 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] Divided Squared 25560.1 29720.6 1.16277
mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 17248.4 21214 3965.6
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided Rooted 62.416 58.6426 1.06435
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Ranked 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
808 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 213.912 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/