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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 7791 to 7840 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1948 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Rooted 65.9292 67.8076 1.02849
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Squared 12197.6 13331.2 1.09294
1949 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] Rooted 65.9292 67.8076 1.02849
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Squared 12197.6 13331.2 1.09294
rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] Ranked 218.794 216.663 1.00984
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] Measured 6230.21 6608.64 1.06074
1950 60s ribosomal protein l23a. [swissprot;acc:p29316] Squared 12632.4 13806.3 1.09293
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Measured 5888.32 6245.89 1.06073
protein x 0001. [refseq;acc:nm_016302] Rooted 65.9292 67.8076 1.02849
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Ranked 215.847 213.747 1.00982
1951 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Squared 12628.2 13801.5 1.09291
fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Measured 5888.32 6245.89 1.06073
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Rooted 65.9292 67.8076 1.02849
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Ranked 205.876 203.873 1.00982
1952 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Rooted 63.7832 65.5999 1.02848
coactosin-like protein. [swissprot;acc:q14019] Measured 5888.32 6245.89 1.06073
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Squared 12627.9 13801.1 1.09291
importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Ranked 211.647 213.724 1.00981
1953 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Squared 12789.3 13977.2 1.09288
salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162] Rooted 63.7832 65.5999 1.02848
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Ranked 125.912 127.146 1.0098
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Measured 5888.32 6245.89 1.06073
1954 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Squared 12789.3 13977.2 1.09288
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Rooted 61.3382 63.0786 1.02837
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Measured 5888.32 6245.89 1.06073
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Ranked 211.632 213.703 1.00979
1955 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Measured 5195.3 5510.67 1.0607
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Rooted 61.3383 63.0785 1.02837
proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] Squared 28220.9 30841.9 1.09287
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Ranked 211.633 213.703 1.00978
1956 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Rooted 61.3383 63.0785 1.02837
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] Measured 4689.78 4973.44 1.06048
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Squared 27944.1 30539.3 1.09287
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Ranked 211.633 213.703 1.00978
1957 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Rooted 69.6016 71.5707 1.02829
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Squared 12050.4 13169.1 1.09284
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Ranked 211.633 213.703 1.00978
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Measured 7019.78 7444.06 1.06044
1958 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Ranked 211.633 213.703 1.00978
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Squared 12175.3 13305.6 1.09284
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Rooted 69.5996 71.5683 1.02829
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] Measured 5448.35 5777.35 1.06039
1959 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Ranked 211.633 213.703 1.00978
fad synthetase. [refseq;acc:nm_025207] Squared 12175.3 13305.6 1.09284
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Rooted 69.6016 71.5707 1.02829
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] Measured 5448.35 5777.35 1.06039
1960 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Squared 12175.3 13305.6 1.09284
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Rooted 69.5947 71.5619 1.02827
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Ranked 211.633 213.703 1.00978
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Measured 5448.35 5777.35 1.06039

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/