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 5658 to 5707 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
708 eif-5a2 protein. [refseq;acc:nm_020390] Squared Subtracted 26472.2 30755.9 4283.7
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Ranked 220.438 209.118 11.32
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Rooted 59.2629 63.7418 4.4789
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Divided 74.8348 80.1352 1.07083
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Measured Subtracted 4775.11 5438.18 663.07
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Squared Divided 19970 23366.8 1.1701
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Measured 5317.78 5944.25 1.11781
709 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Squared Subtracted 17965.8 22243 4277.2
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Ranked 220.438 209.118 11.32
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Measured 5148.71 5811.74 663.03
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Ranked Divided 220.438 209.118 1.05413
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Squared 25114 29386 1.1701
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Rooted Subtracted 66.9416 71.4055 4.4639
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Divided 80.4069 86.1018 1.07083
pp1201 protein. [refseq;acc:nm_022152] Measured 5317.78 5944.25 1.11781
710 alpha-nac protein. [sptrembl;acc:q9h009] Rooted Subtracted 66.9404 71.4035 4.4631
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Ranked Divided 220.438 209.118 1.05413
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Measured Subtracted 2755.15 2094.3 660.85
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Divided 5317.78 5944.25 1.11781
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Ranked Subtracted 220.437 209.118 11.319
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Squared Divided 51519.3 44060.4 1.16929
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] Subtracted 17957.2 22234.1 4276.9
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Rooted Divided 69.2869 74.1856 1.0707
711 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 58.3914 62.5196
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Ranked Subtracted 220.431 209.123 11.308
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Squared Divided 25626.4 29950.3 1.16873
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Measured Subtracted 2759.61 2099.49 660.12
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Rooted 66.9397 71.4023 4.4626
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Measured Divided 5317.78 5944.25 1.11781
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Ranked 232.468 245.048 1.05411
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Squared Subtracted 25114 29386 4272
712 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Divided 25626.4 29950.3 1.16873
di-ras2. [refseq;acc:nm_017594] Rooted Subtracted 66.9397 71.4022 4.4625
dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Ranked 232.762 243.933 11.171
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Divided 220.431 209.123 1.05407
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Measured Subtracted 2760.28 2100.27 660.01
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Squared 25114 29386 4272
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Measured Divided 5317.78 5944.25 1.11781
vinculin (metavinculin). [swissprot;acc:p18206] Rooted 62.9163 67.3603 1.07063
713 dendritic cell protein. [refseq;acc:nm_006360] Ranked 223.121 211.685 1.05402
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Measured Subtracted 5162.52 5822.47 659.95
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Rooted 65.3677 69.828 4.4603
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Squared 25114 29386 4272
guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Divided 25626.4 29950.3 1.16873
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Ranked Subtracted 224.434 235.583 11.149
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Rooted Divided 69.3627 74.2575 1.07057
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Measured 3996.81 4465.61 1.11729
714 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Squared Subtracted 25114 29386 4272
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Measured Divided 5222.71 5834.57 1.11715
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Rooted 61.0082 65.306 1.07045

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/