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 3586 to 3635 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
897 glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Squared 29924.3 34690.9 1.15929
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Measured 5929.48 6531.48 1.10153
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] Rooted 56.2142 59.6282 1.06073
898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Ranked 229.171 238.048 1.03874
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Measured 5929.55 6531.52 1.10152
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] Rooted 56.2142 59.6282 1.06073
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Squared 21156.1 24524.1 1.1592
899 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 29345.7 34004.2 1.15875
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Rooted 66.5785 70.6139 1.06061
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Measured 5929.55 6531.52 1.10152
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Ranked 229.171 238.048 1.03874
900 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Measured 4713.58 4279.17 1.10152
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Rooted 66.5785 70.6139 1.06061
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Ranked 229.171 238.048 1.03874
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] Squared 28068.5 32522.9 1.1587
901 acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Rooted 66.5785 70.6139 1.06061
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Measured 5929.61 6531.55 1.10151
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Ranked 237.62 228.762 1.03872
902 atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] Squared 28068.5 32522.9 1.1587
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Ranked 237.62 228.762 1.03872
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Measured 10246.1 11285.8 1.10147
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Rooted 66.5785 70.6139 1.06061
903 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Ranked 246.354 237.223 1.03849
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Rooted 66.5785 70.6139 1.06061
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Squared 28068.5 32522.9 1.1587
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Measured 4986.58 5492.51 1.10146
904 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Squared 25492.1 29535.4 1.15861
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Ranked 246.354 237.223 1.03849
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Measured 6167.33 6785.98 1.10031
prohibitin. [swissprot;acc:p35232] Rooted 63.4547 67.3003 1.0606
905 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] Squared 27382 31722.9 1.15853
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Ranked 230.768 239.632 1.03841
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Rooted 63.4547 67.3003 1.0606
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Measured 10230.1 11256.2 1.1003
906 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Squared 25498.1 29537.7 1.15843
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Ranked 230.764 239.62 1.03838
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Rooted 61.6325 65.3619 1.06051
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Measured 6165.1 6783.01 1.10023
907 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 11852.9 10773.5 1.10019
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Squared 28767.1 33317.5 1.15818
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Ranked 223.906 215.653 1.03827
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Rooted 53.6328 56.8668 1.0603
908 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Measured 11848.8 10770.3 1.10014
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Rooted 62.6851 66.4615 1.06024
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Squared 28767.1 33317.5 1.15818
tax interaction protein 1. [refseq;acc:nm_014604] Ranked 223.906 215.653 1.03827
909 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Squared 28767.1 33317.5 1.15818
kinesin family member c3. [refseq;acc:nm_005550] Measured 5995.49 6595.35 1.10005
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Rooted 62.6851 66.4615 1.06024

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/