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 Network Comparison Type Hugo Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 12314 to 12363 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Hugo
Value Type
Interaction Map
red
green
network_comparison
770 orphan nuclear receptor tr4 (orphan nuclear receptor tak1). [swissprot;acc:p49116] Divided NR2C2 Ranked Low confidence 206.636 212.168 1.02677
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Subtracted RRAGA High confidence 59 49 10
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] GALNTL1 Low confidence 205.859 200.547 5.312
transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA Rooted High confidence 63.5181 67.7402 4.2221
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided SNRP70 Measured Low confidence 7730.27 8053.27 1.04178
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] no value High confidence 5874.74 6533.34 1.11211
wnt-5b protein precursor. [swissprot;acc:q9h1j7] WNT5B Squared Low confidence 46672 44368.5 1.05192
771 40s ribosomal protein s19. [swissprot;acc:p39019] RPS19 Rooted High confidence 55.6817 59.3786 1.06639
amphiphysin. [swissprot;acc:p49418] Subtracted AMPH Squared Low confidence 46542.4 44304.4 2238
apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] Divided API5 Measured High confidence 5874.74 6533.34 1.11211
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Subtracted ATP5O Squared 24509.4 28571.6 4062.2
cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Divided CYP3A4 Measured Low confidence 8081.2 8418.72 1.04177
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] DNAJB1 Ranked High confidence 210.946 221.225 1.04873
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] QRSL1 Squared 24418 28453.7 1.16528
megf6 (fragment). [sptrembl;acc:o75095] MEGF6 Rooted Low confidence 69.4789 72.3321 1.04107
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] Subtracted TP53RK 76.7049 79.6654 2.9605
poly(a)-specific ribonuclease (deadenylation nuclease); deadenylation nuclease. [refseq;acc:nm_002582] PARN Measured 8068.97 8399.45 330.48
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC Ranked High confidence 59 49 10
ras-related protein ral-a. [swissprot;acc:p11233] Divided RALA Squared Low confidence 46672 44368.5 1.05192
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Subtracted SRP68 Measured High confidence 5622.89 6260.02 637.13
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] no value Rooted 50.5979 46.392 4.2059
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Divided SNAP29 Ranked Low confidence 206.636 212.168 1.02677
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Subtracted LSM5 201.703 196.395 5.308
772 60s ribosomal protein l31. [swissprot;acc:p12947] Divided RPL31 Rooted High confidence 55.6817 59.3786 1.06639
adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Subtracted SLC25A5 Measured Low confidence 8183.08 8513.53 330.45
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] TSFM Rooted 71.1874 74.1471 2.9597
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Divided ETF1 Ranked High confidence 210.946 221.225 1.04873
fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] FAAH Squared 24418 28453.7 1.16528
homolog of yeast maf1. [refseq;acc:nm_032272] Subtracted MAF1 26029.5 30074.5 4045
nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795] Divided NDUFA9 Rooted Low confidence 70.5067 73.4022 1.04107
neurofibromin (neurofibromatosis-related protein nf-1) [contains: neurofibromin truncated]. [swissprot;acc:p21359] no value Squared 47747.4 45390.5 1.05192
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Subtracted DDX56 Measured High confidence 3494.31 4129.6 635.29
protein phosphatase 1, regulatory (inhibitor) subunit 3b. [refseq;acc:nm_024607] Divided PPP1R3B Ranked Low confidence 203.48 198.181 1.02674
ptd002 protein. [refseq;acc:nm_016144] Subtracted COMMD10 Squared 43241.9 41008.5 2233.4
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Ranked High confidence 59 49 10
sec13-related protein. [swissprot;acc:p55735] Divided SEC13 Measured 5874.76 6533.36 1.11211
serine hydrolase-like protein (ec 3.1.-.-). [swissprot;acc:q9h4i8] Subtracted SERHL2 Ranked Low confidence 208.488 203.181 5.307
syntaxin 7. [swissprot;acc:o15400] STX7 Rooted High confidence 61.5022 65.7076 4.2054
zinc finger protein 183. [swissprot;acc:o15541] Divided RNF113A Measured Low confidence 7534.02 7848.32 1.04172
773 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Subtracted AGPAT2 8256.68 8587.03 330.35
60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] MRPL11 Rooted High confidence 50.2583 46.057 4.2013
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] ADSSL1 Low confidence 73.9248 76.8841 2.9593
alpha-n-acetylglucosaminidase precursor (ec 3.2.1.50) (n-acetyl-alpha- glucosaminidase) (nag). [swissprot;acc:p54802] NAGLU Squared 43241.9 41008.5 2233.4
anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN Ranked High confidence 59 49 10
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] no value Low confidence 208.488 203.181 5.307
bup protein. [refseq;acc:nm_012071] Divided COMMD3 Squared 44283.2 42097.7 1.05191
coactosin-like protein. [swissprot;acc:q14019] COTL1 High confidence 24418 28453.7 1.16528
hn1 like. [refseq;acc:nm_144570] HN1L Rooted Low confidence 76.6516 79.7999 1.04107
jm1 protein. [refseq;acc:nm_014008] Subtracted CCDC22 Measured High confidence 5794.8 6427.79 632.99
protein containing cxxc domain 2. [refseq;acc:nm_032590] Divided FBXL10 Ranked Low confidence 202.951 208.378 1.02674

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/