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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Network Comparison Type Gene Value Type description Rank Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 2808 to 2857 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
red
green
network_comparison
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 2552 193.12 193.467 1.0018
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 612 247.47 233.441 1.0601
testis-specific protein tex28. [swissprot;acc:o15482] 802 212.386 221.785 1.04425
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 3021 0.00001 0.00001 1
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 855 178.514 171.42 1.04138
tetratricopeptide repeat protein 1 (tpr repeat protein 1). [swissprot;acc:q99614] 3060 0.00001 0.00001 1
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] 2321 203.909 202.925 1.00485
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] 1747 188.452 190.845 1.0127
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 410 233.376 253.539 1.0864
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 411
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 652 248.994 235.255 1.0584
tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] 1360 223.89 228.805 1.02195
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] 2264 221.599 220.351 1.00566
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] 900 229.171 238.048 1.03874
thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755] 2666 210.136 209.911 1.00107
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] 899 229.171 238.048 1.03874
thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] 2405 221.677 222.489 1.00366
thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757] 2383 212.724 213.574 1.004
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] 1037 228.412 235.609 1.03151
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 1024 205.632 199.266 1.03195
thousand and one amino acid protein kinase. [refseq;acc:nm_004783] 2906 0.00001 0.00001 1
thrombospondin 3 precursor. [swissprot;acc:p49746] 227 239.99 269.234 1.12186
thymic stromal co-transporter. [refseq;acc:nm_033051] 472 248.152 267.226 1.07686
thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142] 2837 0.00001 0.00001 1
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] 2104 209.328 207.813 1.00729
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] 1590 225.119 228.769 1.01621
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 2703 188.435 188.311 1.00066
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 1460 205.817 209.851 1.0196
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] 1621 228.611 225.185 1.01521
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 2816 0.00001 0.00001 1
tigger transposable element derived 6. [refseq;acc:nm_030953] 2853
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 2944
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 133 350 290 1.2069
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 132
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] 2540 217.144 216.699 1.00205
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] 2642 194.097 194.328 1.00119
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] 2073 229.267 227.433 1.00806
trabid protein. [swissprot;acc:q9ugi0] 3210 0.00001 0.00001 1
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] 2031 218.466 216.562 1.00879
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 2322 236.023 234.905 1.00476
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] 2364 212.816 213.697 1.00414
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 1619 227.768 231.246 1.01527
transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] 1618
transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [swissprot;acc:q99081] 2948 0.00001 0.00001 1
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 2940
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] 2279 191.936 190.909 1.00538
transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] 2969 0.00001 0.00001 1
transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481] 3220
transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754] 3164
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 865 211.961 203.814 1.03997

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/