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 2275 to 2324 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1138 golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Subtracted 5790.65 6303.92 513.27
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Divided 1.08864
1139 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] Subtracted 513.27
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Divided 5790.66 6303.95 1.08864
1140 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] Subtracted 5790.65 6303.92 513.27
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Divided 6303.93 1.08864
1141 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Subtracted 6303.92 513.27
1142 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Divided 5789.07 6302.01 1.0886
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Subtracted 5790.65 6303.92 513.27
1143 cda11 protein. [refseq;acc:nm_032026] 5874.11 6387.23 513.12
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Divided 6281.21 6837.61 1.08858
1144 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Subtracted 6011.44 6524.55 513.11
1145 40s ribosomal protein s30. [swissprot;acc:q05472] Divided 5893.97 6416.07 1.08858
importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Subtracted 5789.07 6302.01 512.94
1146 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Divided 6281.21 6837.61 1.08858
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Subtracted 5391.64 5903.72 512.08
1147 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Divided 6281.21 6837.61 1.08858
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Subtracted 5832.13 6343.59 511.46
1148 elks protein. [refseq;acc:nm_015064]
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Divided 6281.21 6837.61 1.08858
1149 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] 6280.74 6837.01 1.08857
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Subtracted 5997.24 6508.62 511.38
1150 cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] 6207.57 6718.7 511.13
mstp028 protein. [refseq;acc:nm_031954] Divided 5838.87 6355.06 1.08841
1151 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 5322.74 5793.15 1.08838
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Subtracted 5998.58 6509.65 511.07
1152 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 5998.69 6509.74 511.05
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Divided 5322.74 5793.15 1.08838
1153 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Subtracted 5913.73 6423.98 510.25
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Divided 5840.01 6355.56 1.08828
1154 tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] 5840.65 6355.84 1.08821
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Subtracted 6004.54 6514.24 509.7
1155 transducin-like enhancer protein 4. [swissprot;acc:q04727] Divided 6270.67 6823.73 1.0882
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Subtracted 5826.34 6335.98 509.64
1156 polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Divided 5840.77 6355.89 1.08819
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Subtracted 5826.29 6335.93 509.64
1157 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 5826.32 6335.95 509.63
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Divided 5418.33 5895.2 1.08801
1158 delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 5489.18 5972.09 1.08797
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Subtracted 5973.95 6483.32 509.37
1159 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 3975.77 4485.05 509.28
kccr13l. [refseq;acc:nm_139179] Divided 5538.8 6025.51 1.08787
1160 dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 3975.77 4485.05 509.28
1161 autoantigen ngp-1. [swissprot;acc:q13823] 3766.14 4274.79 508.65
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Divided 5315.76 5782.63 1.08783
1162 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Subtracted 5799.35 6305.95 506.6
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Divided 5832.13 6343.59 1.0877

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/