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 description Gene Network Comparison Type Value Type Filtered Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 1610 to 1659 of 6456 in total
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
Rank
description
Network Comparison Type
red
network_comparison
green
805 dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Subtracted 212.386 9.399 221.785
806 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Divided 1.04425
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
807 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
808 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 9.274 213.912
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Divided 212.386 1.04425 221.785
809 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Subtracted 233.298 9.273 242.571
syntaxin 16 (syn16). [swissprot;acc:o14662] Divided 212.386 1.04425 221.785
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 9.237 230.957
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 1.04425 221.785
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 9.226 236.467
813 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Divided 212.386 1.04425 221.785
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Subtracted 228.599 9.2 219.399
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 1.04425 221.785
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Subtracted 244.155 9.195 234.96
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 9.131 237.223
syntaxin 1b. [swissprot;acc:q15531] Divided 212.386 1.04425 221.785
816 eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Subtracted 246.354 9.131 237.223
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Divided 212.386 1.04425 221.785
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 9.076 101.613
818 60s ribosomal protein l39. [swissprot;acc:p02404] 234.025 9.067 224.958
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided 168.592 1.04422 161.452
819 60s ribosomal protein l18a. [swissprot;acc:q02543] Subtracted 234.025 9.067 224.958
dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Divided 228.563 1.04421 238.668
820 40s ribosomal protein s19. [swissprot;acc:p39019] Subtracted 234.025 9.067 224.958
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Divided 221.716 1.04413 231.501
821 60s ribosomal protein l31. [swissprot;acc:p12947] Subtracted 234.025 9.067 224.958
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Divided 221.676 1.0441 231.453
822 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 243.067 1.04408 232.805
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Subtracted 55 9 46
823 myosin vc (myosin 5c). [swissprot;acc:q9nqx4]
transcription factor iib. [refseq;acc:nm_013242] Divided 206.068 1.04354 197.471
824 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 55 9 46
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Divided 206.068 1.04354 197.471
825 40s ribosomal protein s3a. [swissprot;acc:p49241] Subtracted 225.689 8.985 234.674
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Divided 206.214 1.04352 197.614
826 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 1.04335 213.912
dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Subtracted 230.811 8.974 239.785
827 jm1 protein. [refseq;acc:nm_014008] 219.762 8.956 210.806
loh1cr12. [refseq;acc:nm_058169] Divided 230.087 1.0431 220.579
828 ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted 135.087 8.954 144.041
unr protein. [swissprot;acc:o75534] Divided 230.087 1.0431 220.579
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 8.948 261.821
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 1.04288 130.259
830 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 231.734 1.0428 222.222

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/