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 11264 to 11313 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
906 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Measured Subtracted 5168.43 4597.44 570.99
907 40s ribosomal protein s19. [swissprot;acc:p39019] Rooted 55.6817 59.3786 3.6969
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Measured Divided 11852.9 10773.5 1.10019
elongation factor 2 (ef-2). [swissprot;acc:p13639] Squared Subtracted 23598.8 27286.9 3688.1
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Divided 28767.1 33317.5 1.15818
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Ranked 223.906 215.653 1.03827
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Subtracted 225.976 218.017 7.959
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Rooted Divided 53.6328 56.8668 1.0603
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Measured Subtracted 3779.92 4348.48 568.56
908 60s ribosomal protein l31. [swissprot;acc:p12947] Rooted 55.6817 59.3786 3.6969
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Measured Divided 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
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Subtracted 23598.8 27286.9 3688.1
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Measured 3721.19 4288.17 566.98
sedlin. [swissprot;acc:o14582] Ranked 129.219 121.261 7.958
tax interaction protein 1. [refseq;acc:nm_014604] Divided 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
atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Rooted Subtracted 62.3496 66.0388 3.6892
kinesin family member c3. [refseq;acc:nm_005550] Measured Divided 5995.49 6595.35 1.10005
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Squared Subtracted 23598.8 27286.9 3688.1
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Measured 3758.67 4322.87 564.2
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 Divided 62.6851 66.4615 1.06024
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Ranked 142.077 136.846 1.03823
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 129.219 121.261 7.958
910 bet3 homolog. [swissprot;acc:o43617]
cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Rooted 67.7551 71.4422 3.6871
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Measured 3766.03 4329.37 563.34
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Squared Divided 19732.4 22852.4 1.15812
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Rooted 55.9078 59.2557 1.05988
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Squared Subtracted 25660.4 29342.7 3682.3
sipl protein. [refseq;acc:nm_018269] Measured Divided 6522.94 7175.18 1.09999
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Ranked 217.168 209.207 1.03805
911 ad24 protein. [refseq;acc:nm_022451] Measured Subtracted 3753.71 4315.95 562.24
bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Squared 22573.3 26254.5 3681.2
ero1-like. [refseq;acc:nm_014584] Ranked Divided 217.168 209.207 1.03805
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Subtracted 225.955 218.015 7.94
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Rooted 58.5869 62.2732 3.6863
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Measured Divided 4982.81 5480.91 1.09996
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Squared 13688.1 15849.2 1.15788
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Rooted 64.1165 67.9451 1.05971
912 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Squared 30826.4 35693.3 1.15788
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Rooted Subtracted 58.5944 62.2766 3.6822
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Ranked 225.939 218.013 7.926
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Measured Divided 4982.81 5480.91 1.09996
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Rooted 64.1184 67.9467 1.05971
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Squared Subtracted 26914.1 30594.2 3680.1
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Measured 3847.31 4409.22 561.91
wd-repeat protein 3. [swissprot;acc:q9unx4] Ranked Divided 243.896 234.96 1.03803
913 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Subtracted 243.297 235.373 7.924

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/