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 713 to 762 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
179 60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878] Divided Low confidence 209.954 221.607 1.0555
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Subtracted 214.779 204.039 10.74
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided High confidence 226.884 194.79 1.16476
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Subtracted 227.357 254.15 26.793
180 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Low confidence 211.506 222.243 10.737
pp3111 protein. [refseq;acc:nm_022156] High confidence 227.357 254.15 26.793
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Divided Low confidence 218.925 207.441 1.05536
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] High confidence 256.228 298.438 1.16474
181 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Low confidence 196.362 206.979 1.05407
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] High confidence 229.818 267.265 1.16294
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Subtracted Low confidence 211.484 222.196 10.712
syntaxin 18. [swissprot;acc:q9p2w9] High confidence 227.357 254.15 26.793
182 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Low confidence 211.475 222.177 10.702
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Divided High confidence 277.546 240.461 1.15422
px serine/threonine kinase. [refseq;acc:nm_017771] Low confidence 196.372 206.947 1.05385
rd protein. [swissprot;acc:p18615] Subtracted High confidence 227.357 254.15 26.793
183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided 228.306 198.011 1.153
bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Low confidence 196.372 206.947 1.05385
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Subtracted High confidence 227.357 254.15 26.793
heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] Low confidence 219.606 208.904 10.702
184 alpha crystallin a chain. [swissprot;acc:p02489] 219.589 208.895 10.694
androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] High confidence 227.357 254.15 26.793
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided 274.027 237.79 1.15239
testis specific, 10. [refseq;acc:nm_025244] Low confidence 196.373 206.946 1.05384
185 adiponectin receptor 2. [refseq;acc:nm_024551] High confidence 281.582 246.371 1.14292
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Subtracted 227.357 254.15 26.793
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Divided Low confidence 212.589 201.755 1.0537
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 211.457 222.138 10.681
186 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided 196.381 206.921 1.05367
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Subtracted 215.723 205.046 10.677
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Divided High confidence 226.582 198.444 1.14179
j domain containing protein 1. [swissprot;acc:q9ukb3] Subtracted 227.357 254.15 26.793
187 alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] Low confidence 219.543 208.868 10.675
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Divided High confidence 226.582 198.444 1.14179
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence 189.373 179.829 1.05307
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Subtracted High confidence 227.357 254.15 26.793
188 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Low confidence 208.591 219.23 10.639
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided High confidence 226.582 198.444 1.14179
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 189.45 179.944 1.05283
189 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Subtracted 196.362 206.979 10.617
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Divided 214.779 204.039 1.05264
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Subtracted High confidence 241.373 267.352 25.979
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 226.582 198.444 1.14179
190 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Low confidence 210.557 200.074 1.0524
fad synthetase. [refseq;acc:nm_025207] Subtracted High confidence 241.373 267.352 25.979
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Low confidence 211.383 221.976 10.593
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided High confidence 226.582 198.444 1.14179
191 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Subtracted 241.373 267.352 25.979
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 226.582 198.444 1.14179

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/