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 Hugo description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1012 to 1061 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
253 NOX4 nadph oxidase 4. [refseq;acc:nm_016931] Divided Low confidence 210.413 201.035 1.04665
254 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Subtracted 218.785 209.763 9.022
MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] High confidence 227.999 204.357 23.642
NOX3 nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Divided Low confidence 210.414 201.035 1.04665
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] High confidence 200.691 179.88 1.11569
255 MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Subtracted 227.999 204.366 23.633
NOX1 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
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted 200.699 191.678 9.021
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided High confidence 200.691 179.88 1.11569
256 MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 204.357
RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 204.37 23.629
SOAT2 sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] Low confidence 208.469 199.455 9.014
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 199.376 190.521 1.04648
257 CMPK 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
DDOST 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 200.691 179.88 1.11569
JAG2 jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Subtracted Low confidence 218.715 209.71 9.005
TPM3 tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Divided 201.316 192.404 1.04632
258 AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Subtracted High confidence 242.14 265.697 23.557
JAG1 jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] Low confidence 218.714 209.709 9.005
MXD4 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
TPM1 tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Low confidence 201.304 192.427 1.04613
259 no value 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
MEF2C myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Low confidence 218.714 209.709 9.005
PDSS1 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Divided 211.794 202.482 1.04599
RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] High confidence 227.999 204.37 1.11562
260 ANKRD7 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] Low confidence 216.855 207.34 1.04589
HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] High confidence 219.421 196.978 1.11394
MED22 surfeit locus protein 5. [swissprot;acc:q15528] Subtracted 242.14 265.696 23.556
MEF2A myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Low confidence 218.715 209.71 9.005
261 ANKRD19 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] Divided 216.845 207.333 1.04588
HS3ST3A1 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
MEF2D myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Subtracted Low confidence 218.713 209.709 9.004
SCAPER zinc finger protein 291. [swissprot;acc:q9by12] High confidence 242.14 265.696 23.556
262 ANKRD30A breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Divided Low confidence 216.842 207.332 1.04587
HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] High confidence 219.421 196.978 1.11394
PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Subtracted 242.14 265.696 23.556
RNF10 ring finger protein 10. [refseq;acc:nm_014868] Low confidence 208.437 199.44 8.997
263 no value sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581] Divided 216.546 207.063 1.0458
HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] High confidence 219.421 196.978 1.11394
SOAT1 sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610] Subtracted Low confidence 208.436 199.44 8.996
TXNDC9 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] High confidence 242.14 265.696 23.556
264 no value 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796
ATP2C1 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
DCPS 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
LEO1 senescence downregulated leo1-like. [refseq;acc:nm_138792] Low confidence 216.546 207.063 1.0458
265 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted High confidence 240.243 263.798 23.555
SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided 225.217 202.459 1.11241
SLC9A7 solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [refseq;acc:nm_032591] Low confidence 216.546 207.063 1.0458
TNKS2 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 214.675 205.692 8.983
266 PHKG2 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] 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
- Hugo is the HGNC identifier if it exists
- 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/