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 Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1875 to 1924 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
938 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Divided 6432.03 5859.25 1.09776
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Subtracted 6690.18 6133.83 556.35
939 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Divided 6432.03 5859.25 1.09776
940 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 6113.35 5568.96 1.09775
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Subtracted 6837.01 6280.74 556.27
941 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Divided 5455.34 4970.21 1.09761
paraspeckle protein 1. [refseq;acc:nm_018282] Subtracted 9685.21 10241.3 556.09
942 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Divided 7240.64 6597.56 1.09747
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Subtracted 6193.07 5637.43 555.64
943 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Divided 7241 6597.98 1.09746
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Subtracted 6193.08 5637.45 555.63
944 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Divided 7241 6597.98 1.09746
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Subtracted 6194.22 5638.64 555.58
945 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Divided 7241 6597.98 1.09746
cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Subtracted 6194.04 5638.46 555.58
946 phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Divided 7241.32 6598.37 1.09744
surfeit locus protein 1. [swissprot;acc:q15526] Subtracted 6194.04 5638.46 555.58
947 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 6194.23 5638.65
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Divided 10750.2 11797.1 1.09738
948 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 5084.24 4633.48 1.09728
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Subtracted 6194.17 5638.59 555.58
949 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] Divided 5084.24 4633.48 1.09728
cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Subtracted 6194.04 5638.46 555.58
950 bystin. [swissprot;acc:q13895] Divided 4697.02 4280.99 1.09718
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Subtracted 6194.04 5638.46 555.58
951 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Divided 5885.48 5364.3 1.09716
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Subtracted 6195.52 5640 555.52
952 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] 6355.71 5800.95 554.76
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Divided 5885.48 5364.3 1.09716
953 casein kinase i alpha s-like. [refseq;acc:nm_145203] 5382.5 4906.33 1.09705
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Subtracted 5750.34 5195.58 554.76
954 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Divided 5382.5 4906.33 1.09705
zinc finger-like protein 9. [refseq;acc:nm_033414] Subtracted 4315.06 3760.8 554.26
955 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
uridine kinase-like 1. [swissprot;acc:q9nwz5] Divided 6086.89 5548.78 1.09698
956 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 5884.89 5364.77 1.09695
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Subtracted 4315.06 3760.8 554.26
957 structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Divided 4917.77 4483.26 1.09692
transducin-like enhancer protein 4. [swissprot;acc:q04727] Subtracted 6823.73 6270.67 553.06
958 block of proliferation 1. [swissprot;acc:q14137] 4348.59 3796.24 552.35
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Divided 4917.77 4483.26 1.09692
959 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Subtracted 6180.37 5628.21 552.16
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Divided 4803.59 4379.28 1.09689
960 protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] 10733.2 11773 1.09688
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Subtracted 6962.22 6410.73 551.49
961 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Divided 10733.2 11773 1.09688
962 transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Subtracted 5723.22 5172.07 551.15
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Divided 10733.2 11773 1.09688

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/