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.


Navigation/Query Panel:
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 4558 to 4607 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
285 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked Divided 1 224.647 203.242 1.10532
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Rooted Subtracted 108.653 100.352 8.301
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Squared Divided 0 208.691 170.202 1.22614
286 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked Subtracted 1 242.593 265.365 22.772
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Measured Divided 0 5497.01 6127.24 1.11465
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Ranked 12228.2 11367.3 1.07573
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 1 224.633 203.251 1.1052
exocyst complex component sec5. [swissprot;acc:q96kp1] Measured 23316 19288.8 1.20878
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Rooted 0 54.8943 59.4407 1.08282
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Squared 188.588 231.109 1.22547
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Rooted Subtracted 16.0012 17.8885 1.8873
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Ranked 11431.4 12244.1 812.7
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Squared 13069.7 13161.9 92.2
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 1 32056.4 39965.8 7909.4
rna-binding protein. [refseq;acc:nm_019027] Measured 4069.83 5252.17 1182.34
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Rooted Divided 51.8717 46.3287 1.11965
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Squared 6693.64 8564.94 1.27956
transforming protein n-ras. [swissprot;acc:p01111] Rooted Subtracted 108.65 100.35 8.3
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Measured 0 939 848 91
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked Divided 1 240.758 266.079 1.10517
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Measured 0 726.245 808.929 1.11385
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted 1 4069.83 5252.17 1182.34
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Squared 0 67.8804 159.002 91.1216
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Ranked 10922.9 11731.8 808.9
fibrillin 3. [refseq;acc:nm_032447] Rooted 119.357 117.512 1.845
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Squared Divided 188.452 230.941 1.22546
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1 6693.64 8564.94 1.27956
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Rooted 51.8714 46.3281 1.11965
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 0 34.7164 32.0874 1.08193
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 1 23303.1 19279.5 1.2087
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Ranked 0 17842.7 16590.3 1.07549
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted 1 225.217 202.459 22.758
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Rooted 97.1967 105.302 8.1053
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Measured 0 2363.32 2454.04 90.72
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared 1 28878.8 36783.5 7904.7
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked Divided 240.758 266.078 1.10517
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 0 14930.6 16053 1.07517
adp-ribosylation factor 3. [swissprot;acc:p16587] Squared Subtracted 33.5285 123.56 90.0315
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Measured Divided 1 23422.4 19380.3 1.20857
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Squared 0 188.176 230.603 1.22546
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted Subtracted 38.0352 36.2234 1.8118
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Squared Divided 1 6693.64 8564.94 1.27956
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Measured 0 1293.73 1161.64 1.11371
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted 1 51.8789 46.3416 1.11949
my016 protein. [sptrembl;acc:q9h3k6] Ranked Subtracted 0 5561.19 6366.91 805.72
Rooted Divided 37.7009 34.862 1.08143
ns1-associated protein 1. [refseq;acc:nm_006372] Measured Subtracted 1 4069.83 5252.17 1182.34
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 0 1631.97 1542.23 89.74
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared 1 28896.2 36767 7870.8
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Rooted 55.8956 63.9636 8.068

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/