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 1013 to 1062 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
254 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Subtracted High confidence 227.999 204.357 23.642
nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Divided Low confidence 210.414 201.035 1.04665
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Subtracted 218.785 209.763 9.022
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Divided High confidence 200.691 179.88 1.11569
255 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Subtracted 227.999 204.366 23.633
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Divided Low confidence 210.413 201.035 1.04665
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted 200.699 191.678 9.021
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided High confidence 200.691 179.88 1.11569
256 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 227.999 204.37 23.629
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Divided 204.357 1.11569
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Low confidence 199.376 190.521 1.04648
sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] Subtracted 208.469 199.455 9.014
257 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Divided High confidence 200.691 179.88 1.11569
jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Subtracted Low confidence 218.715 209.71 9.005
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Divided 201.316 192.404 1.04632
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Subtracted High confidence 242.14 265.697 23.557
258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] Low confidence 218.714 209.709 9.005
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Divided High confidence 227.999 204.366 1.11564
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Low confidence 201.304 192.427 1.04613
259 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Subtracted High confidence 242.14 265.696 23.556
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 227.999 204.37 1.11562
myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Subtracted Low confidence 218.714 209.709 9.005
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Divided 211.794 202.482 1.04599
260 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] 216.855 207.34 1.04589
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] High confidence 219.421 196.978 1.11394
myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Subtracted Low confidence 218.715 209.71 9.005
surfeit locus protein 5. [swissprot;acc:q15528] High confidence 242.14 265.696 23.556
261 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] Divided Low confidence 216.845 207.333 1.04588
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] High confidence 219.421 196.978 1.11394
myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Subtracted Low confidence 218.713 209.709 9.004
zinc finger protein 291. [swissprot;acc:q9by12] High confidence 242.14 265.696 23.556
262 breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Divided Low confidence 216.842 207.332 1.04587
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] High confidence 219.421 196.978 1.11394
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Subtracted 242.14 265.696 23.556
ring finger protein 10. [refseq;acc:nm_014868] Low confidence 208.437 199.44 8.997
263 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Divided High confidence 219.421 196.978 1.11394
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Subtracted 242.14 265.696 23.556
sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581] Divided Low confidence 216.546 207.063 1.0458
sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610] Subtracted 208.436 199.44 8.996
264 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] High confidence 243.24 266.796 23.556
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Low confidence 218.661 209.669 8.992
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Divided High confidence 219.421 196.978 1.11394
senescence downregulated leo1-like. [refseq;acc:nm_138792] Low confidence 216.546 207.063 1.0458
265 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted High confidence 240.243 263.798 23.555
solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [refseq;acc:nm_032591] Divided Low confidence 216.546 207.063 1.0458
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] High confidence 225.217 202.459 1.11241
tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2] Subtracted Low confidence 214.675 205.692 8.983
266 calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] Divided 214.887 205.509 1.04563
phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [swissprot;acc:p15735] Subtracted 217.756 226.722 8.966

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/