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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 530 to 579 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
265 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
266 SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] High confidence 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 DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 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
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 1.04519
269 PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] High confidence 241.373 267.352 1.10763
SOAT1 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
270 FLAD1 fad synthetase. [refseq;acc:nm_025207] High confidence 241.373 267.352 1.10763
RNF10 ring finger protein 10. [refseq;acc:nm_014868] Low confidence 208.437 199.44 1.04511
271 no value 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
TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Low confidence 201.219 192.595 1.04478
272 LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] High confidence 241.373 267.352 1.10763
OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Low confidence 217.69 208.421 1.04447
273 CDC73 parafibromin. [refseq;acc:nm_024529] 214.015 204.916 1.0444
PAPSS1 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] High confidence 241.373 267.352 1.10763
274 KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Low confidence 209.532 200.653 1.04425
POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] High confidence 241.373 267.352 1.10763
275 NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Low confidence 199.66 191.203 1.04423
PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] High confidence 241.373 267.352 1.10763
276 NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Low confidence 199.939 191.474 1.04421
SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] High confidence 241.13 266.969 1.10716
277 no value 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 267.642 1.10665
cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 211.912 202.965 1.04408
278 RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] High confidence 241.399 267.088 1.10642
SLC7A10 asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82] Low confidence 205.006 196.369 1.04398
279 BTBD14B transcriptional repressor nac1. [refseq;acc:nm_052876] 202.309 211.2 1.04395
RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] High confidence 252.644 228.42 1.10605
280 MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 228.356 1.10578
TFCP2L1 lbp-9. [refseq;acc:nm_014553] Low confidence 219.758 210.509 1.04394
281 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] High confidence 241.808 267.335 1.10557
TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Low confidence 219.749 210.503 1.04392
282 AMY1C alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 219.742 210.498 1.04391
RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] High confidence 252.39 228.297 1.10553
283 RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 267.346 1.10552
UBP1 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Low confidence 219.722 210.484 1.04389
284 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] High confidence 224.657 203.235 1.10541
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] Low confidence 214.675 205.692 1.04367
285 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 224.647 203.242 1.10532
TAF4 transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Low confidence 202.354 211.175 1.04359
286 NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] High confidence 224.633 203.251 1.1052
TAF4B transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] Low confidence 202.356 211.174 1.04358
287 GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 210.132 201.397 1.04337
RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] High confidence 240.758 266.079 1.10517
288 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 266.078
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Low confidence 200.288 192.004 1.04314
289 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] High confidence 272.781 246.892 1.10486
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Low confidence 209.31 200.66 1.04311
290 LAPTM4B lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] 210 201.325 1.04309

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/