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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2401 to 2450 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
601 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 Subtracted Low confidence 216.554 210.642 5.912
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] CROT Divided 208.67 202.603 1.02995
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN Subtracted High confidence 207.26 194.346 12.914
vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] VPS39 Divided 206.274 218.792 1.06069
602 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] MAP4
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 Subtracted Low confidence 216.552 210.641 5.911
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR High confidence 207.26 194.346 12.914
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] SH2D3C Divided Low confidence 201.426 195.579 1.0299
603 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] BCAR3 201.427 195.587 1.02986
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 Subtracted High confidence 207.27 194.368 12.902
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] LEF1 Divided 225.829 212.945 1.0605
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 Subtracted Low confidence 216.552 210.641 5.911
604 60s ribosomal protein l15. [swissprot;acc:p39030] RPL15 Divided High confidence 217.862 230.978 1.0602
60s ribosomal protein l36. [swissprot;acc:q9y3u8] RPL36 Low confidence 205.116 211.234 1.02983
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 Subtracted High confidence 207.272 194.371 12.901
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Low confidence 216.552 210.641 5.911
605 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] CDK2AP1 216.501 210.602 5.899
histone h2b.c (h2b/c). [swissprot;acc:q99880] HIST1H2BL Divided High confidence 247.47 233.441 1.0601
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] LEF1 Subtracted 225.829 212.945 12.884
probable rna-dependent helicase p72 (dead-box protein p72) (dead-box protein 17). [swissprot;acc:q92841] DDX17 Divided Low confidence 204.837 198.913 1.02978
606 dolichyl-p-man:man(5)glcnac(2)-pp-dolichyl mannosyltransferase (ec 2.4.1.-) (dol-p-man dependent alpha(1-3)-mannosyltransferase) (not56-like protein). [swissprot;acc:q92685] no value 200.085 194.301 1.02977
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] HIST2H2BA High confidence 247.47 233.441 1.0601
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] WASL Subtracted 207.309 194.452 12.857
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] G3BP1 Low confidence 211.28 217.166 5.886
607 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] BBS7 207.763 201.882 5.881
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] no value Divided High confidence 247.47 233.441 1.0601
probable rna-dependent helicase p68 (dead-box protein p68) (dead-box protein 5). [swissprot;acc:p17844] DDX5 Low confidence 204.832 198.916 1.02974
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] SCOC Subtracted High confidence 216.731 229.549 12.818
608 ba161i19.3 (similar to ribosomal protein l36). [sptrembl;acc:q8wx03] no value Divided Low confidence 205.117 211.213 1.02972
dynein light chain 2. [refseq;acc:nm_080677] DYNLL2 Subtracted High confidence 216.731 229.549 12.818
histone h2b. [refseq;acc:nm_175055] no value Divided 247.47 233.441 1.0601
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] SSB Subtracted Low confidence 205.472 199.6 5.872
609 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] no value High confidence 226.523 213.786 12.737
histone h2b.s (h2b/s). [swissprot;acc:p57053] Divided 247.47 233.441 1.0601
protein disulfide isomerase a4 precursor (ec 5.3.4.1) (protein erp-72) (erp72). [swissprot;acc:p13667] PDIA4 Subtracted Low confidence 204.388 198.518 5.87
tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] TP63 Divided 191.867 186.346 1.02963
610 histone h2b.d (h2b/d). [swissprot;acc:q99877] no value High confidence 247.47 233.441 1.0601
inositol oxygenase (ec 1.13.99.1) (myo-inositol oxygenase) (aldehyde reductase-like 6) (renal-specific oxidoreductase) (kidney-specific protein 32). [swissprot;acc:q9ugb7] MIOX Subtracted Low confidence 212.062 206.202 5.86
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] SOS1 High confidence 205.74 193.021 12.719
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] TP73 Divided Low confidence 191.871 186.351 1.02962
611 cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] TP53 191.875 186.357 1.02961
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] HIST3H3 High confidence 247.47 233.441 1.0601
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] no value Subtracted 228.986 216.276 12.71
wd repeat and fyve domain containing 3 isoform 1. [refseq;acc:nm_014991] WDFY3 Low confidence 205.129 199.271 5.858
612 protein disulfide isomerase a4 precursor (ec 5.3.4.1) (protein erp-72) (erp72). [swissprot;acc:p13667] PDIA4 Divided 204.388 198.518 1.02957
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] SH2D3C Subtracted 201.426 195.579 5.847
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] SOS2 High confidence 205.89 193.183 12.707
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] HIST1H2BA Divided 247.47 233.441 1.0601
613 histone h2b.e (h2b/e). [swissprot;acc:q99879] no value
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] FAIM2 Low confidence 203.626 197.78 1.02956

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/