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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3208 to 3257 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
802 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
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 26254.5 1.16308
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Measured 6455.02 7167.96 1.11045
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 212.386 221.785 1.04425
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 51.3516 1.06474
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] 74.3877 79.1931 1.0646
a kindred of iglon. [refseq;acc:nm_173808] Ranked 212.386 221.785 1.04425
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 7517.97 1.11036
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Squared 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
60s ribosomal protein l39. [swissprot;acc:p02404] 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
806 40s ribosomal protein s26. [swissprot;acc:p02383] Rooted 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
807 40s ribosomal protein s19. [swissprot;acc:p39019] Measured 4708.61 5226.71 1.11003
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 29720.6 1.16277
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 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
808 60s ribosomal protein l31. [swissprot;acc:p12947] Measured 4708.61 5226.71 1.11003
atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Rooted 62.416 58.6426 1.06435
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Ranked 212.386 221.785 1.04425
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Squared 24818.5 28857.3 1.16273
809 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] 15511.8 18033.2 1.16255
syntaxin 16 (syn16). [swissprot;acc:o14662] Ranked 212.386 221.785 1.04425
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Rooted 62.416 58.6426 1.06435
wd-repeat protein 3. [swissprot;acc:q9unx4] Measured 4039.81 4484.22 1.11001
810 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Ranked 212.386 221.785 1.04425
grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Squared 15511.8 18033.2 1.16255
jm1 protein. [refseq;acc:nm_014008] Measured 5794.8 6427.79 1.10923
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Rooted 51.7169 55.044 1.06433
811 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 73.9102 78.6514 1.06415
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Measured 6000.07 6655.11 1.10917
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] Squared 15511.8 18033.2 1.16255
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Ranked 212.386 221.785 1.04425
812 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Rooted 51.6795 54.9937 1.06413
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] Squared 15511.8 18033.2 1.16255
target of myb protein 1. [swissprot;acc:o60784] Measured 5640.79 6255.85 1.10904
813 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Ranked 212.386 221.785 1.04425
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Rooted 51.7273 55.0399 1.06404
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] Measured 5641.11 6255.99 1.109
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Squared 15511.8 18033.2 1.16255
814 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 6585.44 7655.13 1.16243
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Ranked 212.386 221.785 1.04425
target of myb protein 1. [swissprot;acc:o60784] Rooted 61.6688 65.6175 1.06403
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Measured 5641.12 6255.99 1.109
815 midasin (midas-containing protein). [swissprot;acc:q9nu22] 4483.08 4971.62 1.10897

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/