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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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 [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1330 to 1379 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
665 HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Subtracted 214.254 202.166 12.088
666 EIF3I 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
HES1 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 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 250.465 238.38 12.085
ECH1 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Divided 229.072 216.576 1.0577
668 ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
FTSJ3 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 no value presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 232.601 244.534 11.933
SYN1 synapsin i (brain protein 4.1). [swissprot;acc:p17600] Divided 229.072 216.576 1.0577
670 GNL2 autoantigen ngp-1. [swissprot;acc:q13823] 250.302 236.817 1.05694
RANP1 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Subtracted 232.601 244.534 11.933
671 no value presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided 210.739 199.398 1.05688
672 no value dok-like protein. [refseq;acc:nm_024872] Subtracted 216.504 204.622 11.882
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Divided 210.739 199.398 1.05688
673 CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 226.497 214.355 1.05664
DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Subtracted 216.504 204.622 11.882
674 DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Divided 226.497 214.355 1.05664
675 FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Subtracted 216.504 204.622 11.882
SIM1 single-minded homolog 1. [swissprot;acc:p81133] Divided 226.497 214.355 1.05664
676 MRTO4 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
POLR2G dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Divided 232.469 245.613 1.05654
677 FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Subtracted 245.246 233.483 11.763
LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided 228.944 216.745 1.05628
678 PPIL4 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
SNX5 sorting nexin 5. [swissprot;acc:q9y5x3] Divided 208.482 220.175 1.05609
679 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 132.413 125.389 1.05602
SNX5 sorting nexin 5. [swissprot;acc:q9y5x3] Subtracted 208.482 220.175 11.693
680 HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided 132.413 125.389 1.05602
SFRS18 sr rich protein. [refseq;acc:nm_032870] Subtracted 225.293 213.64 11.653
681 HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Divided 132.413 125.389 1.05602
SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Subtracted 220.593 208.987 11.606
682 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 132.413 125.389 1.05602
NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Subtracted 246.055 234.458 11.597
683 HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Divided 132.413 125.389 1.05602
OSTF1 osteoclast stimulating factor 1. [swissprot;acc:q92882] Subtracted 231.809 243.289 11.48
684 HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Divided 132.413 125.389 1.05602
PFAS 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 ATIC 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]
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Divided 132.413 125.389 1.05602
686 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
PAICS 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 EIF3M dendritic cell protein. [refseq;acc:nm_006360] 223.121 211.685 11.436
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Divided 132.413 125.389 1.05602
688 CPXM2 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Subtracted 223.121 211.685 11.436
POLR2D dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Divided 237.554 250.823 1.05586
689 CPN1 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] Subtracted 223.121 211.685 11.436
TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Divided 135.379 128.225 1.05579
690 CPZ cpz gene product. [refseq;acc:nm_003652] Subtracted 223.121 211.685 11.436

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
- Hugo is the HGNC identifier if it exists
- 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/