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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2625 to 2674 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
657 GIPC1 Measured rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 6079.26 6824.47 1.12258
SORBS3 Rooted vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 64.75 69.8065 1.07809
SPRY2 Squared sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 27174.1 31992.4 1.17731
SYN3 Ranked synapsin iii. [swissprot;acc:o14994] 229.072 216.576 1.0577
658 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
EIF3B Rooted eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 52.7523 56.8686 1.07803
PARS2 Squared similar to trna synthetase class ii. [refseq;acc:nm_152268] 22293.8 26242.6 1.17713
SHROOM2 Measured apical-like protein (apxl protein). [swissprot;acc:q13796] 6088.77 6834.87 1.12254
659 HEY1 Ranked hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] 229.072 216.576 1.0577
MRPS9 Rooted 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 51.7081 47.9816 1.07767
OTC Squared ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 24614 28973.4 1.17711
SHROOM3 Measured shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 6089.21 6835.34 1.12253
660 no value u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 5575.18 6254.85 1.12191
ABLIM2 Ranked actin binding lim protein 2. [refseq;acc:nm_032432] 229.072 216.576 1.0577
FIP1L1 Rooted fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 133.216 123.627 1.07756
NDUFB9 Squared nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 33024.9 38867.8 1.17692
661 ALAD delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 22223.1 26152.4 1.17681
HEYL Ranked hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 229.072 216.576 1.0577
NXF5 Rooted nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 68.8243 74.1496 1.07738
SLU7 Measured step ii splicing factor slu7. [refseq;acc:nm_006425] 5575.18 6254.85 1.12191
662 no value Squared ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 23947.4 28163.7 1.17607
NXF3 Rooted nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 68.8237 74.1484 1.07737
PARD6G Measured partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 6374.65 7145.59 1.12094
SYN2 Ranked synapsin ii. [swissprot;acc:q92777] 229.072 216.576 1.0577
663 ACRC Squared acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 23947.7 28163.9 1.17606
MRRF Ranked mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 229.072 216.576 1.0577
NXF1 Rooted nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 68.8197 74.1413 1.07733
TUB Measured tubby protein homolog. [swissprot;acc:p50607] 6374.65 7145.59 1.12094
664 NET1 Rooted neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 51.6042 55.574 1.07693
PEX5 Ranked peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 229.072 216.576 1.0577
PRKCI Measured protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 6374.65 7145.59 1.12094
SUMO3 Squared ubiquitin-like protein smt3a. [swissprot;acc:p55854] 23948 28164.1 1.17605
665 ARHGEF3 Rooted 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] 51.6042 55.574 1.07693
HEY2 Ranked hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 229.072 216.576 1.0577
LSM6 Squared u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 18960.3 22298 1.17604
NUMB Measured numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] 6374.65 7145.59 1.12094
666 HES1 Ranked transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 229.072 216.576 1.0577
SLC37A1 Squared glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 29224 34362.1 1.17582
TBC1D5 Measured tbc1 domain family member 5. [swissprot;acc:q92609] 6374.65 7145.59 1.12094
UTP20 Rooted down-regulated in metastasis. [refseq;acc:nm_014503] 51.6042 55.574 1.07693
667 ECH1 Ranked delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 229.072 216.576 1.0577
PRODH Squared proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] 29224 34362.1 1.17582
TULP1 Measured tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] 6374.65 7145.59 1.12094
UQCRFSL1 Rooted ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 51.2483 47.5889 1.0769
668 no value Squared isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 23969.3 28175.3 1.17547
ABLIM1 Ranked actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 229.072 216.576 1.0577
ACADVL Rooted acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 95.4476 102.785 1.07687
VPS29 Measured vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] 6374.65 7145.59 1.12094
669 HPRT1 Rooted hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 79.931 86.0693 1.07679
LSM4 Squared u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 18548.7 21798.2 1.17519

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/