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 2275 to 2324 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
143 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted Subtracted 1 105.205 92.2415 12.9635
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured Divided 9275.1 7089.65 1.30826
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted 15427.2 13572.8 1854.4
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Rooted 0 30.6682 26.8335 3.8347
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Ranked Divided 11124.8 13005.3 1.16904
importin 4. [refseq;acc:nm_024658] Rooted 16.4019 13.9084 1.17928
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Ranked Subtracted 9545 7868 1677
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted Divided 1 55.6161 66.7332 1.19989
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Squared 124319 86848.2 1.43145
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Measured 0 187 144 1.29861
seven in absentia homolog 1. [refseq;acc:nm_003031] Squared Subtracted 14383.6 13569.2 814.4
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked 1 240.133 211.382 28.751
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Squared Divided 0 634.375 361.911 1.75285
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Subtracted 1 86600.9 65229.9 21371
144 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Ranked 239.35 267.915 28.565
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Squared 86600.9 65229.9 21371
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Ranked Divided 0 11123.4 13000.1 1.16872
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Measured Subtracted 1612.86 1843.92 231.06
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Ranked Divided 1 265.686 319.651 1.20312
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted Subtracted 105.205 92.2415 12.9635
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Measured 4133.47 5945.32 1811.85
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared Divided 0 207.597 118.463 1.75242
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Subtracted 4275.32 3463.45 811.87
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Measured Divided 1 3349.9 4362.61 1.30231
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Rooted Subtracted 0 8.48528 12.2882 3.80292
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared Divided 1 123324 86277.9 1.42938
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 66.7332 1.19989
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 0 9.72761 8.25872 1.17786
uridine kinase-like 1. [swissprot;acc:q9nwz5] Measured 633.433 821.711 1.29723
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Ranked Subtracted 12225.7 13893.1 1667.4
145 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared Divided 255.854 146.067 1.75162
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Subtracted 1 86600.9 65229.9 21371
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Rooted Divided 55.6161 66.7332 1.19989
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared Subtracted 0 975.125 178.265 796.86
lamin b2. [swissprot;acc:q03252] Ranked 12135.4 13802 1666.6
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Rooted 82.3645 86.1594 3.7949
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Ranked 1 239.336 267.881 28.545
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Measured Divided 0 287.903 372.961 1.29544
methyltransferase like 2. [refseq;acc:nm_018396] Rooted 5.56776 6.55744 1.17775
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared 1 310840 442993 1.42515
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Measured Subtracted 4136.36 5943.56 1807.2
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked Divided 265.639 319.546 1.20293
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Rooted Subtracted 105.205 92.2415 12.9635
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] Measured 0 2162.33 1932 230.33
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Ranked Divided 7955.61 6817.49 1.16694
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 1 16771.5 12889.1 1.30122
146 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 1.30082
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Ranked 0 12577.8 14662.1 1.16571
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] Measured Subtracted 17356 17126 230
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Divided 291.639 377.574 1.29466

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/