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 3608 to 3657 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
451 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Squared 1 17543.3 21222.5 1.20972
452 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted 50.4595 46.0415 1.09596
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Measured 0 1527.36 1504.85 1.01496
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Ranked 1 224.161 207.972 1.07784
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Rooted 0 29.7773 29.2679 1.0174
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Ranked 14010.2 13737.2 1.01987
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Squared 24278.9 23613 1.0282
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 1 17543.3 21222.5 1.20972
zinc finger-like protein 9. [refseq;acc:nm_033414] Measured 3760.8 4315.06 1.14738
453 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 0 1337.29 1356.52 1.01438
bystin. [swissprot;acc:q13895] Rooted 29.2217 28.7356 1.01692
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] Squared 71297.2 69420.1 1.02704
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Measured 1 3760.8 4315.06 1.14738
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Squared 31620.5 38250.7 1.20968
surfeit locus protein 5. [swissprot;acc:q15528] Rooted 50.4595 46.0413 1.09596
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Ranked 0 14010.2 13737.2 1.01987
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 1 224.161 207.972 1.07784
454 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Squared 0 74.4463 72.5416 1.02626
gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Rooted 1 50.4595 46.0412 1.09596
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Measured 3760.8 4315.06 1.14738
lats homolog 1. [refseq;acc:nm_004690] Ranked 0 13933.5 14204.8 1.01947
seven in absentia homolog 1. [refseq;acc:nm_003031] Rooted 28.462 28.9328 1.01654
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Squared 1 31620.5 38250.7 1.20968
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Measured 0 3219.3 3174.79 1.01402
455 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Squared 6970.13 6794.39 1.02587
acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 1 31597.8 38216.9 1.20948
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Measured 4890.51 5610.95 1.14731
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Ranked 210.225 226.578 1.07779
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Measured 0 2403.53 2371.24 1.01362
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Ranked 13933.5 14204.8 1.01947
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Rooted 137.437 139.628 1.01594
zinc finger protein 291. [swissprot;acc:q9by12] 1 50.4595 46.0413 1.09596
456 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Ranked 210.225 226.578 1.07779
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] Rooted 0 77.1368 75.9272 1.01593
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Squared 1282.67 1314.42 1.02475
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] Measured 17356 17126 1.01343
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] 1 4890.51 5610.95 1.14731
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Squared 10933.6 13219.6 1.20908
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Rooted 50.4595 46.0413 1.09596
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Ranked 0 16416.1 16721.6 1.01861
457 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Measured 1562.36 1541.69 1.01341
fibrillin 3. [refseq;acc:nm_032447] Rooted 119.357 117.512 1.0157
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Measured 1 4890.51 5610.95 1.14731
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Squared 10936.1 13221.9 1.20901
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Rooted 50.4595 46.0413 1.09596
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Squared 0 1967.66 1925.55 1.02187
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Ranked 1 210.225 226.578 1.07779
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] 0 16416.1 16721.6 1.01861
458 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Rooted 28.0847 28.5146 1.01531

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/