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.


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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 1344 to 1393 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
672 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
688 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 237.554 250.823 1.05586
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Subtracted 223.121 211.685 11.436
689 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Divided 135.379 128.225 1.05579
690 cpz gene product. [refseq;acc:nm_003652] Subtracted 223.121 211.685 11.436
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Divided 220.593 208.987 1.05553
691 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 217.602 206.195 1.05532
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Subtracted 223.121 211.685 11.436
692 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Divided 217.602 206.195 1.05532
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Subtracted 223.121 211.685 11.436
693 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 217.602 206.195 11.407
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Divided 222.554 234.847 1.05524
694 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Subtracted 217.602 206.195 11.407
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Divided 241.907 229.35 1.05475
695 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Subtracted 210.739 199.398 11.341
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Divided 226.135 214.405 1.05471
696 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted 210.739 199.398 11.341
sr rich protein. [refseq;acc:nm_032870] Divided 225.293 213.64 1.05455
697 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 220.444 209.113 1.05419

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/