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 Value Type description Hugo Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 712 to 761 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
network_comparison
green
178 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] GNG4 Subtracted Low confidence 211.51 10.742 222.252
179 60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878] RPL6 Divided 209.954 1.0555 221.607
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] DNALI1 Subtracted 214.779 10.74 204.039
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value Divided High confidence 226.884 1.16476 194.79
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] PAH Subtracted 227.357 26.793 254.15
180 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] GNG3 Low confidence 211.506 10.737 222.243
pp3111 protein. [refseq;acc:nm_022156] DUS1L High confidence 227.357 26.793 254.15
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] DCHS1 Divided Low confidence 218.925 1.05536 207.441
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP High confidence 256.228 1.16474 298.438
181 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 Low confidence 196.362 1.05407 206.979
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 High confidence 229.818 1.16294 267.265
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] GNG8 Subtracted Low confidence 211.484 10.712 222.196
syntaxin 18. [swissprot;acc:q9p2w9] STX18 High confidence 227.357 26.793 254.15
182 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] GNG5 Low confidence 211.475 10.702 222.177
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 Divided High confidence 277.546 1.15422 240.461
px serine/threonine kinase. [refseq;acc:nm_017771] PXK Low confidence 196.372 1.05385 206.947
rd protein. [swissprot;acc:p18615] no value Subtracted High confidence 227.357 26.793 254.15
183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Divided 228.306 1.153 198.011
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] no value Low confidence 196.372 1.05385 206.947
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] GSTO1 Subtracted High confidence 227.357 26.793 254.15
heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] HSPB6 Low confidence 219.606 10.702 208.904
184 alpha crystallin a chain. [swissprot;acc:p02489] CRYAA 219.589 10.694 208.895
androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] AIG1 High confidence 227.357 26.793 254.15
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 Divided 274.027 1.15239 237.79
testis specific, 10. [refseq;acc:nm_025244] TSGA10 Low confidence 196.373 1.05384 206.946
185 adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 High confidence 281.582 1.14292 246.371
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] ATP5F1 Subtracted 227.357 26.793 254.15
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] no value Divided Low confidence 212.589 1.0537 201.755
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 211.457 10.681 222.138
186 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP Divided 196.381 1.05367 206.921
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] COG5 Subtracted 215.723 10.677 205.046
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] FLNB Divided High confidence 226.582 1.14179 198.444
j domain containing protein 1. [swissprot;acc:q9ukb3] DNAJC12 Subtracted 227.357 26.793 254.15
187 alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] CRYAB Low confidence 219.543 10.675 208.868
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Divided High confidence 226.582 1.14179 198.444
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] no value Low confidence 189.373 1.05307 179.829
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] SNX13 Subtracted High confidence 227.357 26.793 254.15
188 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] CYC1 Low confidence 208.591 10.639 219.23
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Divided High confidence 226.582 1.14179 198.444
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] RPS6KC1 Low confidence 189.45 1.05283 179.944
189 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 Subtracted 196.362 10.617 206.979
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] DNALI1 Divided 214.779 1.05264 204.039
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] PCYT1A Subtracted High confidence 241.373 25.979 267.352
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Divided 226.582 1.14179 198.444
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] FMO5 Low confidence 210.557 1.0524 200.074
fad synthetase. [refseq;acc:nm_025207] FLAD1 Subtracted High confidence 241.373 25.979 267.352
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 Low confidence 211.383 10.593 221.976
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 Divided High confidence 226.582 1.14179 198.444
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] no value Subtracted 241.373 25.979 267.352

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/