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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1025 to 1074 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
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
RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] High confidence 243.12 266.662 23.542
SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Divided 241.07 267.88 1.11121
WDR92 calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] Low confidence 214.887 205.509 1.04563
267 no value 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Subtracted High confidence 243.12 266.661 23.541
cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 211.912 202.965 8.947
DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Divided High confidence 241.07 267.88 1.11121
TNS1 tensin. [refseq;acc:nm_022648] Low confidence 215.258 205.872 1.04559
268 EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] High confidence 271.016 244.167 1.10996
PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Subtracted 241.625 265.136 23.511
SOAT2 sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] Divided Low confidence 208.469 199.455 1.04519
TPM3 tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Subtracted 201.316 192.404 8.912
269 no value 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] High confidence 241.625 265.136 23.511
BTBD14B transcriptional repressor nac1. [refseq;acc:nm_052876] Low confidence 202.309 211.2 8.891

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/