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 [...,...].
Gene Rank Network Comparison Type description Value Type green Filtered network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
Filtered  : 1
Interaction Map  : High confidence
Rank
Network Comparison Type
description
Value Type
green
network_comparison
red
801 Subtracted werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Squared 24595.9 3982.8 20613.1
802 Divided pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 23416.5 1.16319 20131.3
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 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
Subtracted 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
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Ranked 221.785 9.399 212.386
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Rooted 86.2754 4.0913 82.1841
803 Divided 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 26254.5 1.16308 22573.3
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Measured 7167.96 1.11045 6455.02
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 221.785 1.04425 212.386
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 51.3516 1.06474 54.6759
Subtracted calsyntenin-1 precursor. [swissprot;acc:o94985] 86.2754 4.0913 82.1841
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 1390.33 611.163 779.167
syntaxin 1b. [swissprot;acc:q15531] Ranked 221.785 9.399 212.386
transforming protein rhoc (h9). [swissprot;acc:p08134] Squared 23960.7 3973.1 19987.6
804 Divided 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 79.1931 1.0646 74.3877
a kindred of iglon. [refseq;acc:nm_173808] Ranked 221.785 1.04425 212.386
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Measured 7517.97 1.11036 6770.78
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Squared 29022.6 1.16302 24954.5
Subtracted melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Ranked 221.785 9.399 212.386
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Measured 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
805 Divided 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
60s ribosomal protein l39. [swissprot;acc:p02404] 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
Subtracted 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 23960.7 3973.1 19987.6
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] 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 Divided 40s ribosomal protein s26. [swissprot;acc:p02383] 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
Subtracted maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 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 Divided 40s ribosomal protein s19. [swissprot;acc:p39019] Measured 5226.71 1.11003 4708.61
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 29720.6 1.16277 25560.1
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 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
Subtracted chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 1390.33 611.163 779.167
gk001 protein. [refseq;acc:nm_020198] Rooted 86.2753 4.0913 82.184
mad protein (max dimerizer). [swissprot;acc:q05195] Squared 21214 3965.6 17248.4
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] Ranked 227.796 9.275 218.521
808 Divided 60s ribosomal protein l31. [swissprot;acc:p12947] Measured 5226.71 1.11003 4708.61

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/