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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2654 to 2703 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
664 PEX5 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Ranked 229.072 216.576 1.0577
PRKCI protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Measured 6374.65 7145.59 1.12094
SUMO3 ubiquitin-like protein smt3a. [swissprot;acc:p55854] Squared 23948 28164.1 1.17605
665 ARHGEF3 rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Rooted 51.6042 55.574 1.07693
HEY2 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Ranked 229.072 216.576 1.0577
LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Squared 18960.3 22298 1.17604
NUMB numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Measured 6374.65 7145.59 1.12094
666 HES1 transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Ranked 229.072 216.576 1.0577
SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Squared 29224 34362.1 1.17582
TBC1D5 tbc1 domain family member 5. [swissprot;acc:q92609] Measured 6374.65 7145.59 1.12094
UTP20 down-regulated in metastasis. [refseq;acc:nm_014503] Rooted 51.6042 55.574 1.07693
667 ECH1 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Ranked 229.072 216.576 1.0577
PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Squared 29224 34362.1 1.17582
TULP1 tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Measured 6374.65 7145.59 1.12094
UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Rooted 51.2483 47.5889 1.0769
668 no value isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Squared 23969.3 28175.3 1.17547
ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Ranked 229.072 216.576 1.0577
ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Rooted 95.4476 102.785 1.07687
VPS29 vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Measured 6374.65 7145.59 1.12094
669 HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Rooted 79.931 86.0693 1.07679
LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Squared 18548.7 21798.2 1.17519
NUMBL numb-like protein (numb-r). [swissprot;acc:q9y6r0] Measured 6374.65 7145.59 1.12094
SYN1 synapsin i (brain protein 4.1). [swissprot;acc:p17600] Ranked 229.072 216.576 1.0577
670 no value dok-like protein. [refseq;acc:nm_024872] Squared 28911 33971.3 1.17503
GNL2 autoantigen ngp-1. [swissprot;acc:q13823] Ranked 250.302 236.817 1.05694
POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Rooted 51.2122 47.5637 1.07671
TULP3 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Measured 6374.65 7145.59 1.12094
671 DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Squared 28911 33971.3 1.17503
NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Ranked 210.739 199.398 1.05688
PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Rooted 68.6822 73.8955 1.0759
VPS35 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Measured 6374.65 7145.59 1.12094
672 DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Squared 28911 33971.3 1.17503
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Ranked 210.739 199.398 1.05688
POLR1B dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Rooted 51.4203 47.7936 1.07588
PRKCZ protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Measured 6374.65 7145.59 1.12094
673 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 6933.17 7766.54 1.1202
CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Ranked 226.497 214.355 1.05664
FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Squared 28911 33971.3 1.17503
PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Rooted 132.156 122.835 1.07588
674 no value apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Squared 42467.5 36156.7 1.17454
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Measured 5549.2 6215.42 1.12006
EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Rooted 132.114 122.802 1.07583
HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Ranked 226.497 214.355 1.05664
675 BCKDK [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Squared 22347.6 26247.3 1.1745
PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Rooted 132.063 122.761 1.07577
SIM1 single-minded homolog 1. [swissprot;acc:p81133] Ranked 226.497 214.355 1.05664
SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Measured 5549.2 6215.42 1.12006
676 CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Rooted 132.467 123.158 1.07559
DPP10 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Squared 22337.3 26234.1 1.17445
POLR2G dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Ranked 232.469 245.613 1.05654

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/