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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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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6462 to 6511 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1616 n-acetylglutamate synthase. [refseq;acc:nm_153006] Ranked 223.179 226.611 1.01538
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Squared 15399.5 17067.9 1.10834
twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] Rooted 62.3332 64.4896 1.03459
1617 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Squared 15399.5 17067.9 1.10834
lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663] Measured 6035.6 6464.5 1.07106
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Rooted 62.3332 64.4896 1.03459
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Ranked 221.045 217.699 1.01537
1618 60s ribosomal protein l18. [swissprot;acc:q07020] Squared 15399.5 17067.9 1.10834
f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Rooted 64.1847 66.4025 1.03455
proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721] Measured 6035.6 6464.5 1.07106
transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] Ranked 227.768 231.246 1.01527
1619 adp-ribosylation factor-like protein 1. [swissprot;acc:p40616] Measured 6035.6 6464.5 1.07106
f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Rooted 64.1847 66.4025 1.03455
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Squared 31022.4 34382.7 1.10832
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Ranked 227.768 231.246 1.01527
1620 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Measured 6296.52 6743.85 1.07104
heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] Squared 26833.7 29737.4 1.10821
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Rooted 64.4022 66.6218 1.03446
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Ranked 228.611 225.185 1.01521
1621 calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] Rooted 58.9585 60.9832 1.03434
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Measured 5520.36 5911.98 1.07094
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Squared 14652.3 16236.8 1.10814
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Ranked 228.611 225.185 1.01521
1622 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] Rooted 61.6526 63.7646 1.03426
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Squared 14652.3 16236.8 1.10814
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Ranked 228.611 225.185 1.01521
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Measured 6153.79 6589.52 1.07081
1623 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Rooted 64.49 66.699 1.03425
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Ranked 228.611 225.185 1.01521
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Squared 14652.3 16236.8 1.10814
transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] Measured 6449.02 6905.56 1.07079
1624 rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251] Rooted 61.8805 64.0002 1.03425
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Ranked 230.643 227.194 1.01518
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Measured 4102.1 4392.15 1.07071
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Squared 14652.3 16236.8 1.10814
1625 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Ranked 217.446 214.2 1.01515
ran binding protein 11. [refseq;acc:nm_016338] Rooted 64.5022 66.7097 1.03422
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Squared 14652.3 16236.8 1.10814
zinc finger protein 277. [swissprot;acc:q9nrm2] Measured 4102.1 4392.15 1.07071
1626 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] Squared 14652.3 16236.8 1.10814
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Measured 6157.13 6591.53 1.07055
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] Rooted 64.0671 66.2596 1.03422
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Ranked 217.446 214.2 1.01515
1627 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Measured 6038.46 6463.9 1.07046
dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] Rooted 62.2195 64.3478 1.03421
homeobox protein barh-like 2. [swissprot;acc:q9umq3] Squared 14652.3 16236.8 1.10814
pp1201 protein. [refseq;acc:nm_022152] Ranked 217.446 214.2 1.01515
1628 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] Squared 27762.4 30763.9 1.10811
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Measured 5920.55 6337.28 1.07039
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Ranked 217.446 214.2 1.01515

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/