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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1844 to 1893 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
231 mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Divided Low confidence 1 220.722 210.645 1.04784
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Subtracted High confidence 226.411 202.088 24.323
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 9.483
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Divided High confidence 0 12364.8 11207.9 1.10322
zinc finger protein 226. [swissprot;acc:q9nyt6] Low confidence 4254.87 4851.67 1.14026
232 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted High confidence 12448.9 11393.9 1055
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 1 226.401 202.094 24.307
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Divided Low confidence 214.032 204.284 1.04772
cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Subtracted 208.851 199.38 9.471
g protein-coupled receptor 142. [refseq;acc:nm_181790] 0 9957.01 11067.8 1110.79
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Divided High confidence 12394.7 11240.2 1.10271
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 1 239.336 267.879 1.11926
zinc finger protein 33a (zinc finger protein kox31) (ha0946). [swissprot;acc:q06730] Low confidence 0 4255.19 4852.02 1.14026
233 60s acidic ribosomal protein p1. [swissprot;acc:p05386] High confidence 9586.97 10560 1.1015
60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted 1 235.727 259.984 24.257
acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Low confidence 0 10129.7 11238.6 1108.9
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Divided High confidence 1 239.32 267.842 1.11918
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Low confidence 209.649 200.129 1.04757
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Subtracted 201.41 191.974 9.436
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] High confidence 0 10367 9320.25 1046.75
zinc finger protein 347 (zinc finger 1111). [swissprot;acc:q96se7] Divided Low confidence 4255.83 4852.69 1.14025
234 40s ribosomal protein s23. [swissprot;acc:p39028] Subtracted High confidence 1 243.944 268.195 24.251
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided 287.41 256.835 1.11905
cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Low confidence 208.851 199.38 1.0475
dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Subtracted 210.504 201.086 9.418
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] 0 12808.6 11717.8 1090.8
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] Divided High confidence 16614 18296 1.10124
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Subtracted 7502.08 6461.83 1040.25
zinc finger protein 93 (zinc finger protein htf34). [refseq;acc:nm_145312] Divided Low confidence 4255.59 4852.44 1.14025
235 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Subtracted High confidence 1 243.944 268.195 24.251
40s ribosomal protein s29. [swissprot;acc:p30054] 0 11035.3 9997.71 1037.59
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Divided 14554.5 16027.9 1.10123
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 1 227.357 254.15 1.11785
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Subtracted Low confidence 0 12808.6 11717.8 1090.8
u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] 1 202.727 193.31 9.417
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Divided 202.654 193.53 1.04715
zinc finger protein 157 (hzf22). [swissprot;acc:p51786] 0 4255.83 4852.69 1.14025
236 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Subtracted 1 210.487 201.076 9.411
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 24.224
keratin associated protein 9.2. [refseq;acc:nm_031961] 0 10551.1 11579.9 1028.8
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Divided Low confidence 1 212.056 202.524 1.04707
pp3111 protein. [refseq;acc:nm_022156] High confidence 227.357 254.15 1.11785
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 0 15245.4 16788.5 1.10122
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Subtracted Low confidence 13627.5 12538.5 1089
zinc finger protein 92 (zinc finger protein htf12) (fragment). [swissprot;acc:q03936] Divided 4255.83 4852.69 1.14025
237 alanine-glyoxylate aminotransferase 2-like 1. [refseq;acc:nm_031279] Subtracted 12706.6 13789.7 1083.1
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 High confidence 9984 9067 1.10114
diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Subtracted Low confidence 1 210.443 201.051 9.392
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] High confidence 0 10551.6 11573.7 1022.1
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 1 242.011 266.18 24.169

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/