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 Network Comparison Type Value Type Interaction Map green Filtered network_comparison red
Results: HTML CSV LaTeX Showing element 12864 to 12913 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
Interaction Map
green
network_comparison
red
804 zinc finger protein 291. [swissprot;acc:q9by12] Subtracted Squared Low confidence 43667.8 2204.4 45872.2
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] Divided Rooted High confidence 79.1513 1.0645 74.3557
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Subtracted Squared 23960.7 3973.1 19987.6
60s ribosomal protein l39. [swissprot;acc:p02404] Divided 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
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Rooted Low confidence 74.9692 1.0408 72.0306
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared High confidence 17890 1.16284 15384.8
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Subtracted Ranked 221.785 9.399 212.386
early hematopoietic zinc finger. [refseq;acc:nm_015461] Low confidence 199.706 5.208 204.914
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Divided Measured 8162.73 1.04143 7837.99
interferon-related developmental regulator 1 (nerve growth factor- inducible protein pc4). [swissprot;acc:o00458] Subtracted 8035.7 326.32 7709.38
myeloid leukemia factor 1 (myelodysplasia-myeloid leukemia factor 1). [swissprot;acc:p58340] Rooted 76.7095 2.9402 73.7693
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured High confidence 1390.33 611.163 779.167
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Squared Low confidence 43667.8 2204.4 45872.2
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Rooted High confidence 86.2753 4.0913 82.184
sorting nexin 16. [swissprot;acc:p57768] Divided Squared Low confidence 41772.3 1.05119 43910.5
synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Ranked 193.399 1.02635 198.496
806 40s ribosomal protein s26. [swissprot;acc:p02383] Rooted High confidence 58.6426 1.06435 62.4161
60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] Subtracted Squared Low confidence 44079.6 2203.1 46282.7
60s ribosomal protein l18a. [swissprot;acc:q02543] Divided Measured High confidence 5226.71 1.11003 4708.61
glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Squared Low confidence 45485.5 1.05118 47813.4
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked High confidence 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
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 276.773 9.326 267.447
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Divided Measured Low confidence 8726.61 1.04137 8379.95
mosaic protein lgn. [swissprot;acc:p81274] Subtracted Ranked 202.355 5.205 207.56
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured High confidence 1390.33 611.163 779.167
protein hspc163. [swissprot;acc:q9p003] Rooted Low confidence 78.896 2.9402 75.9558
protein kinase, lysine deficient 1; kinase deficient protein. [refseq;acc:nm_018979] Divided 73.4673 1.0408 70.5871
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Subtracted High confidence 86.2753 4.0913 82.184
transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 23960.7 3973.1 19987.6
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Measured Low confidence 8260.54 326.2 7934.34
vacuolar atp synthase subunit c (ec 3.6.3.14) (v-atpase c subunit) (vacuolar proton pump c subunit). [swissprot;acc:p21283] Divided Ranked 197.173 1.02635 202.369
807 40s ribosomal protein s19. [swissprot;acc:p39019] Measured High confidence 5226.71 1.11003 4708.61
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Subtracted Rooted Low confidence 74.9692 2.9386 72.0306
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured High confidence 1390.33 611.163 779.167
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Divided Low confidence 8614.36 1.04132 8272.57
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 44873.3 1.05117 47169.4
exonuclease nef-sp. [refseq;acc:nm_030941] Rooted 73.4673 1.0408 70.5871
gk001 protein. [refseq;acc:nm_020198] Subtracted High confidence 86.2753 4.0913 82.184
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 29720.6 1.16277 25560.1
mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 21214 3965.6 17248.4
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided Rooted 58.6426 1.06435 62.416
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Ranked Low confidence 195.631 1.02633 200.782
nadp-dependent malic enzyme, mitochondrial precursor (ec 1.1.1.40) (nadp-me) (malic enzyme 3). [swissprot;acc:q16798] Subtracted Measured 8602.07 326.16 8275.91
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Ranked 198.706 5.201 203.907
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Divided High confidence 221.785 1.04425 212.386
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 227.796 9.275 218.521
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Squared Low confidence 44519 2202 46721
808 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] Ranked High confidence 213.912 9.274 223.186

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/