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.


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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 Value Type description Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
network_comparison
green
801 Rooted protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Subtracted 65.0565 4.0968 69.1533
802 Measured chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 779.167 611.163 1390.33
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Divided 6455.66 1.11047 7168.82
Ranked synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Subtracted 212.386 9.399 221.785
testis-specific protein tex28. [swissprot;acc:o15482] Divided 1.04425
Squared cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Subtracted 19987.6 3973.1 23960.7
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 20131.3 1.16319 23416.5
Rooted 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] 54.6759 1.06474 51.3516
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 82.1841 4.0913 86.2754
803 Measured doc-1 related protein (doc-1r). [swissprot;acc:o75956] 779.167 611.163 1390.33
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 6455.02 1.11045 7167.96
Ranked similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] 212.386 1.04425 221.785
syntaxin 1b. [swissprot;acc:q15531] Subtracted 9.399
Squared 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 22573.3 1.16308 26254.5
transforming protein rhoc (h9). [swissprot;acc:p08134] Subtracted 19987.6 3973.1 23960.7
Rooted calsyntenin-1 precursor. [swissprot;acc:o94985] 82.1841 4.0913 86.2754
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 54.6759 1.06474 51.3516
804 Measured nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 6770.78 1.11036 7517.97
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 779.167 611.163 1390.33
Ranked a kindred of iglon. [refseq;acc:nm_173808] Divided 212.386 1.04425 221.785
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Subtracted 9.399
Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 19987.6 3973.1 23960.7
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Divided 24954.5 1.16302 29022.6
Rooted 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] 74.3877 1.0646 79.1931
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] Subtracted 82.1841 4.0913 86.2754
805 Measured 60s ribosomal protein l39. [swissprot;acc:p02404] Divided 4708.61 1.11003 5226.71
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Subtracted 779.167 611.163 1390.33
Ranked ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Divided 212.386 1.04425 221.785
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Subtracted 9.399
Squared 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 19987.6 3973.1 23960.7
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Divided 15384.8 1.16284 17890
Rooted 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] 74.3557 1.0645 79.1513
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Subtracted 82.184 4.0913 86.2753
806 Measured 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 4708.61 1.11003 5226.71
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Subtracted 779.167 611.163 1390.33
Ranked inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Divided 212.386 1.04425 221.785
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Subtracted 267.447 9.326 276.773
Squared inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Divided 25555.4 1.16278 29715.4
transforming protein rhoa (h12). [swissprot;acc:p06749] Subtracted 19987.6 3973.1 23960.7
Rooted 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 62.4161 1.06435 58.6426
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Subtracted 82.184 4.0913 86.2753
807 Measured 40s ribosomal protein s19. [swissprot;acc:p39019] Divided 4708.61 1.11003 5226.71
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted 779.167 611.163 1390.33
Ranked palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Divided 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] Subtracted 218.521 9.275 227.796
Squared 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 25560.1 1.16277 29720.6
mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 17248.4 3965.6 21214
Rooted gk001 protein. [refseq;acc:nm_020198] 82.184 4.0913 86.2753
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided 62.416 1.06435 58.6426
808 Measured 60s ribosomal protein l31. [swissprot;acc:p12947] 4708.61 1.11003 5226.71

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/