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 1613 to 1662 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
807 palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Divided 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
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Divided 212.386 221.785 1.04425
809 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Subtracted 233.298 242.571 9.273
syntaxin 16 (syn16). [swissprot;acc:o14662] Divided 212.386 221.785 1.04425
810 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Subtracted 240.194 230.957 9.237
811 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Divided 212.386 221.785 1.04425
812 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
putatative 28 kda protein. [refseq;acc:nm_020143] Subtracted 227.241 236.467 9.226
813 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Divided 212.386 221.785 1.04425
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Subtracted 228.599 219.399 9.2
814 synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Divided 212.386 221.785 1.04425
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Subtracted 244.155 234.96 9.195
815 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 246.354 237.223 9.131
syntaxin 1b. [swissprot;acc:q15531] Divided 212.386 221.785 1.04425
816 eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Subtracted 246.354 237.223 9.131
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Divided 212.386 221.785 1.04425
817 dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Subtracted 110.689 101.613 9.076
818 60s ribosomal protein l39. [swissprot;acc:p02404] 234.025 224.958 9.067
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided 168.592 161.452 1.04422
819 60s ribosomal protein l18a. [swissprot;acc:q02543] Subtracted 234.025 224.958 9.067
dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Divided 228.563 238.668 1.04421
820 40s ribosomal protein s19. [swissprot;acc:p39019] Subtracted 234.025 224.958 9.067
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Divided 221.716 231.501 1.04413
821 60s ribosomal protein l31. [swissprot;acc:p12947] Subtracted 234.025 224.958 9.067
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Divided 221.676 231.453 1.0441
822 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 243.067 232.805 1.04408
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Subtracted 55 46 9
823 myosin vc (myosin 5c). [swissprot;acc:q9nqx4]
transcription factor iib. [refseq;acc:nm_013242] Divided 206.068 197.471 1.04354
824 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 55 46 9
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Divided 206.068 197.471 1.04354
825 40s ribosomal protein s3a. [swissprot;acc:p49241] Subtracted 225.689 234.674 8.985
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Divided 206.214 197.614 1.04352
826 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 213.912 1.04335
dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Subtracted 230.811 239.785 8.974
827 jm1 protein. [refseq;acc:nm_014008] 219.762 210.806 8.956
loh1cr12. [refseq;acc:nm_058169] Divided 230.087 220.579 1.0431
828 ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted 135.087 144.041 8.954
unr protein. [swissprot;acc:o75534] Divided 230.087 220.579 1.0431
829 dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] Subtracted 252.873 261.821 8.948
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Divided 135.844 130.259 1.04288
830 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 231.734 222.222 1.0428
wd-repeat protein 3. [swissprot;acc:q9unx4] Subtracted 243.896 234.96 8.936
831 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 229.171 238.048 8.877
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Divided 231.734 222.222 1.0428

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/