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 [...,...].
Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1551 to 1600 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Interaction Map
Filtered
red
green
network_comparison
388 scratch; scratch 1. [refseq;acc:nm_031309] High confidence 0 1398.21 1339.9 1.04352
transcription factor sp1. [swissprot;acc:p08047] Low confidence 2175.63 1956.84 1.11181
389 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 1 8159.97 8595.12 1.05333
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] High confidence 0 11512.3 12011.7 1.04338
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 1 4533.74 5279.4 1.16447
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Low confidence 0 1796.05 1616.77 1.11089
390 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] High confidence 11512.3 12011.7 1.04338
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Low confidence 1482.03 1646.15 1.11074
rw1 protein (fragment). [swissprot;acc:q92545] High confidence 1 4533.74 5279.4 1.16447
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Low confidence 6983.51 7354.87 1.05318
391 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 0 1100.34 991.072 1.11025
seven in absentia homolog 1. [refseq;acc:nm_003031] High confidence 2221.04 2316.94 1.04318
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 1 3658.76 3144.39 1.16358
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Low confidence 8552.2 9004.53 1.05289
392 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] High confidence 0 229.211 219.891 1.04238
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 1 3641.89 4236.95 1.16339
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Low confidence 0 2417.64 2682.87 1.10971
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 1 7781.34 8192.41 1.05283
393 cryptochrome 1 (photolyase-like). [refseq;acc:nm_004075] 8673.83 9132.05
dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 0 1148.04 1036.1 1.10804
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] High confidence 1 4490.28 5222.25 1.16301
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 0 2131.42 2218.51 1.04086
394 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 1 4490.28 5222.25 1.16301
histone h2b.d (h2b/d). [swissprot;acc:q99877] 0 2131.52 2218.58 1.04084
mitochondrial carrier protein mgc4399. [refseq;acc:nm_032315] Low confidence 747.346 827.684 1.1075
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] 1 7679.4 8084.79 1.05279
395 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] 8552.34 9003.72 1.05278
histone h2b.s (h2b/s). [swissprot;acc:p57053] High confidence 0 2131.83 2218.82 1.04081
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 1 4532.73 5269.33 1.16251
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Low confidence 0 2092.19 2315.26 1.10662
396 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 1 7680.02 8085.19 1.05276
histone h2b. [refseq;acc:nm_175055] High confidence 0 2131.91 2218.89 1.0408
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 1 6563.65 7627.29 1.16205
zinc finger protein 232. [swissprot;acc:q9uny5] Low confidence 0 1052.99 952.163 1.10589
397 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] 1 7679.55 8084.63 1.05275
histone h2b.e (h2b/e). [swissprot;acc:q99879] High confidence 0 2131.93 2218.9 1.04079
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 1 5367.04 6233.12 1.16137
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Low confidence 0 1267.5 1399.84 1.10441
398 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] 1 7680.47 8085.46 1.05273
histone h2b.c (h2b/c). [swissprot;acc:q99880] High confidence 0 2132.04 2218.98 1.04078
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Low confidence 135.294 149.371 1.10405
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] High confidence 1 5084.26 5904.1 1.16125
399 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Low confidence 7680.62 8085.57 1.05272
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] High confidence 0 548.5 527.5 1.03981
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 1 5201.41 4479.76 1.16109
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Low confidence 0 250.379 226.797 1.10398
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] High confidence 1 5201.41 4479.76 1.16109
mad protein (max dimerizer). [swissprot;acc:q05195] Low confidence 6970.25 7337.73 1.05272
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] High confidence 0 548.5 527.5 1.03981
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Low confidence 1326.18 1201.37 1.10389

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/