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.


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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1075 to 1124 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
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] Divided 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
KHDRBS3 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
RNF10 ring finger protein 10. [refseq;acc:nm_014868] Divided 208.437 199.44 1.04511
RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] Subtracted High confidence 241.612 265.119 23.507
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] Divided 241.373 267.352 1.10763
SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Subtracted 243.072 266.559 23.487
TPM1 tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Low confidence 201.304 192.427 8.877
TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Divided 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
MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 242.83 266.248 23.418
OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided Low confidence 217.69 208.421 1.04447
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 199.376 190.521 8.855
273 BEST1 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 37.318 28.4944 8.8236
CDC73 parafibromin. [refseq;acc:nm_024529] Divided 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
POLR2B 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
274 BEST4 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 37.3475 28.5242 8.8233
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Divided 209.532 200.653 1.04425
MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Subtracted High confidence 242.744 266.07 23.326
POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Divided 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
RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Subtracted 242.473 265.756 23.283
TAF4 transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Low confidence 202.354 211.175 8.821
276 DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] High confidence 258.437 235.183 23.254
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided Low confidence 199.939 191.474 1.04421
SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] High confidence 241.13 266.969 1.10716
TAF4B transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] Subtracted Low confidence 202.356 211.174 8.818
277 no value 40s ribosomal protein s29. [swissprot;acc:p30054] Divided High confidence 241.849 267.642 1.10665
cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 211.912 202.965 1.04408
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 37.9984 29.1831 8.8153
RPL4 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] High confidence 239.277 262.434 23.157
278 BEST2 vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence 37.9984 29.1831 8.8153
MYEF2 myelin gene expression factor 2. [refseq;acc:nm_016132] High confidence 235.383 258.476 23.093
RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 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
GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 210.132 201.397 8.735
PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] High confidence 242.66 265.715 23.055
RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 252.644 228.42 1.10605
280 LAPTM4B lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] Subtracted Low confidence 210 201.325 8.675
MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Divided High confidence 252.512 228.356 1.10578
TFCP2L1 lbp-9. [refseq;acc:nm_014553] Low confidence 219.758 210.509 1.04394
TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted High confidence 267.208 244.168 23.04
281 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 241.808 267.335 1.10557
MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Subtracted 242.159 265.104 22.945
TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Divided Low confidence 219.749 210.503 1.04392
TMEM115 pl6 protein (placental protein 6). [swissprot;acc:q12893] Subtracted 209.995 201.322 8.673

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/