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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1325 to 1374 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
663 mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Divided 229.072 216.576 1.0577
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Subtracted 214.256 202.141 12.115
664 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Divided 229.072 216.576 1.0577
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Subtracted 214.256 202.141 12.115
665 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Divided 229.072 216.576 1.0577
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Subtracted 214.254 202.166 12.088
666 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 250.465 238.38 12.085
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Divided 229.072 216.576 1.0577
667 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 250.465 238.38 12.085
668 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Divided 229.072 216.576 1.0577
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Subtracted 244.495 232.419 12.076
669 presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 232.601 244.534 11.933
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Divided 229.072 216.576 1.0577
670 autoantigen ngp-1. [swissprot;acc:q13823] 250.302 236.817 1.05694
gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Subtracted 232.601 244.534 11.933
671 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided 210.739 199.398 1.05688
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Subtracted 232.601 244.534 11.933
672 dok-like protein. [refseq;acc:nm_024872] 216.504 204.622 11.882
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Divided 210.739 199.398 1.05688
673 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Subtracted 216.504 204.622 11.882
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Divided 226.497 214.355 1.05664
674 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Subtracted 216.504 204.622 11.882
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Divided 226.497 214.355 1.05664
675 single-minded homolog 1. [swissprot;acc:p81133]
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Subtracted 216.504 204.622 11.882
676 dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Divided 232.469 245.613 1.05654
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Subtracted 245.84 257.636 11.796
677 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 245.246 233.483 11.763
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided 228.944 216.745 1.05628
678 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Subtracted 226.135 214.405 11.73
sorting nexin 5. [swissprot;acc:q9y5x3] Divided 208.482 220.175 1.05609
679 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 132.413 125.389 1.05602
sorting nexin 5. [swissprot;acc:q9y5x3] Subtracted 208.482 220.175 11.693
680 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided 132.413 125.389 1.05602
sr rich protein. [refseq;acc:nm_032870] Subtracted 225.293 213.64 11.653
681 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Divided 132.413 125.389 1.05602
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Subtracted 220.593 208.987 11.606
682 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 132.413 125.389 1.05602
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Subtracted 246.055 234.458 11.597
683 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Divided 132.413 125.389 1.05602
osteoclast stimulating factor 1. [swissprot;acc:q92882] Subtracted 231.809 243.289 11.48
684 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Divided 132.413 125.389 1.05602
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Subtracted 223.58 235.027 11.447
685 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Divided 132.413 125.389 1.05602
686 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Subtracted 223.58 235.027 11.447
687 dendritic cell protein. [refseq;acc:nm_006360] 223.121 211.685 11.436
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Divided 132.413 125.389 1.05602

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/