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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1130 to 1179 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
142 CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted Subtracted 105.205 92.2415 12.9635
JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 7523.39 1885.19
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Divided 9276.47 7090.37 1.30832
PPIB peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Squared Subtracted 86600.9 65229.9 21371
PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted Divided 55.6161 66.7332 1.19989
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Ranked 59 49 1.20408
THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 239.99 269.234 29.244
143 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured Divided 9275.1 7089.65 1.30826
ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Ranked 59 49 1.20408
CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Measured Subtracted 15427.2 13572.8 1854.4
OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Squared 86600.9 65229.9 21371
PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Divided 124319 86848.2 1.43145
PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted 55.6161 66.7332 1.19989
SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked Subtracted 240.133 211.382 28.751
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted 105.205 92.2415 12.9635
144 COX4I1 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
CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Ranked 239.35 267.915 28.565
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Divided 265.686 319.651 1.20312
SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 66.7332 1.19989
TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Measured Subtracted 4133.47 5945.32 1811.85
TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared Divided 123324 86277.9 1.42938
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Measured 3349.9 4362.61 1.30231
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted Subtracted 105.205 92.2415 12.9635
145 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 55.6161 66.7332 1.19989
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared 310840 442993 1.42515
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 16771.5 12889.1 1.30122
CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Rooted Subtracted 105.205 92.2415 12.9635
COX4I2 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Squared 86600.9 65229.9 21371
KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked Divided 265.639 319.546 1.20293
SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Subtracted 239.336 267.881 28.545
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Measured 4136.36 5943.56 1807.2
146 CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Ranked 239.336 267.879 28.543
KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted 41.6734 28.9323 12.7411
KCNIP2 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] Ranked Divided 265.632 319.531 1.20291
PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted 55.0737 66.0298 1.19894
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared 103496 146848 1.41888
STAM2 signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Subtracted 86281 65058.3 21222.7
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Measured Divided 11068 8508.5 1.30082
XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 2671 871 1800
147 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Ranked Divided 50.7983 42.3003 1.2009
ATPBD1C protein x 0004. [refseq;acc:nm_016301] Measured Subtracted 2671 871 1800
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 11068 8508.5 1.30082
CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Ranked Subtracted 239.32 267.842 28.522
CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 12.7342
FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Divided 42.0574 50.4237 1.19893
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Squared Subtracted 55630.4 76083.7 20453.3
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Divided 103496 146848 1.41888
148 no value ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Subtracted 70011 49783 20228
FLNB 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] Ranked 226.582 198.444 28.138
FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Rooted Divided 42.0577 50.424 1.19892

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/