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 11214 to 11263 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
900 ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Squared Subtracted 28335.4 32042.6 3707.2
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Ranked Divided 229.171 238.048 1.03874
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] Squared 28068.5 32522.9 1.1587
901 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Rooted Subtracted 51.7081 47.9816 3.7265
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] Squared Divided 28068.5 32522.9 1.1587
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Measured Subtracted 6080.91 6653.52 572.61
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Rooted Divided 66.5785 70.6139 1.06061
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Measured 5929.61 6531.55 1.10151
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Squared Subtracted 22017.1 25721.9 3704.8
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Ranked 212.028 204.055 7.973
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] Divided 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
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Rooted Subtracted 62.309 58.5957 3.7133
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Ranked Divided 237.62 228.762 1.03872
di-ras2. [refseq;acc:nm_017594] Subtracted 212.028 204.055 7.973
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Measured Divided 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
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Squared Subtracted 22535.2 26238.4 3703.2
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Measured 3729.02 4301.58 572.56
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 Divided 246.354 237.223 1.03849
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Measured Subtracted 6077.65 6649.22 571.57
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Rooted 60.6175 64.3272 3.7097
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Divided 66.5785 70.6139 1.06061
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Squared Subtracted 22075.1 25775.1 3700
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Divided 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
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Ranked Subtracted 217.168 209.207 7.961
904 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Squared Divided 25492.1 29535.4 1.15861
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Ranked Subtracted 243.312 235.351 7.961
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Divided 246.354 237.223 1.03849
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Measured Subtracted 6213.51 6785.04 571.53
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Squared 24426.8 28125 3698.2
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Measured Divided 6167.33 6785.98 1.10031
prohibitin. [swissprot;acc:p35232] Rooted 63.4547 67.3003 1.0606
tax interaction protein 1. [refseq;acc:nm_014604] Subtracted 60.6175 64.3272 3.7097
905 60s ribosomal protein l39. [swissprot;acc:p02404] 55.6817 59.3786 3.6969
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 Divided 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
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Measured Subtracted 5168.43 4597.44 570.99
ero1-like. [refseq;acc:nm_014584] Ranked 217.168 209.207 7.961
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Squared 29952.7 33648.1 3695.4
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Rooted Divided 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 60s ribosomal protein l18a. [swissprot;acc:q02543] Rooted Subtracted 55.6817 59.3786 3.6969
arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Squared Divided 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
pbk1 protein. [sptrembl;acc:o76021] Subtracted 243.312 235.353 7.959
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Rooted Divided 61.6325 65.3619 1.06051
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Measured 6165.1 6783.01 1.10023
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Squared Subtracted 29952.7 33648.1 3695.4

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/