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 1051 to 1100 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
263 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
ribosomal protein l10-like protein. [refseq;acc:nm_080746] High confidence 243.12 266.662 23.542
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Divided 241.07 267.88 1.11121
267 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Subtracted 243.12 266.661 23.541
cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 211.912 202.965 8.947
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
tensin. [refseq;acc:nm_022648] Low confidence 215.258 205.872 1.04559
268 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] High confidence 271.016 244.167 1.10996
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Subtracted 241.625 265.136 23.511
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
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Subtracted 201.316 192.404 8.912
269 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] High confidence 241.625 265.136 23.511
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Divided 241.373 267.352 1.10763
sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610] Low confidence 208.436 199.44 1.04511
transcriptional repressor nac1. [refseq;acc:nm_052876] Subtracted 202.309 211.2 8.891
270 40s ribosomal protein s3. [swissprot;acc:p23396] High confidence 241.612 265.119 23.507
fad synthetase. [refseq;acc:nm_025207] Divided 241.373 267.352 1.10763
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Subtracted Low confidence 209.532 200.653 8.879
ring finger protein 10. [refseq;acc:nm_014868] Divided 208.437 199.44 1.04511
271 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] High confidence 241.373 267.352 1.10763
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Subtracted 243.072 266.559 23.487
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Low confidence 201.304 192.427 8.877
tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Divided 201.219 192.595 1.04478
272 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] High confidence 241.373 267.352 1.10763
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 242.83 266.248 23.418
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided Low confidence 217.69 208.421 1.04447
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 199.376 190.521 8.855
273 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 37.318 28.4944 8.8236
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [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:o43252] Divided High confidence 241.373 267.352 1.10763
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Subtracted 243.208 266.617 23.409
parafibromin. [refseq;acc:nm_024529] Divided Low confidence 214.015 204.916 1.0444
274 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Subtracted High confidence 242.744 266.07 23.326
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Divided Low confidence 209.532 200.653 1.04425
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] High confidence 241.373 267.352 1.10763
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Subtracted Low confidence 37.3475 28.5242 8.8233
275 40s ribosomal protein s5. [swissprot;acc:p46782] High confidence 242.473 265.756 23.283
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Divided 241.373 267.352 1.10763
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Low confidence 199.66 191.203 1.04423
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Subtracted 202.354 211.175 8.821

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/