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.


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 2251 to 2300 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
282 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Ranked Subtracted 242.159 265.104 22.945
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured 677.5 1865.5 1188
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Divided 3119.98 2579.49 1.20953
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Rooted 57.9819 64.9302 1.11984
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Squared 59704 76460.4 1.28066
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Rooted Subtracted 108.671 100.365 8.306
283 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Ranked 242.37 265.255 22.885
60s ribosomal protein l11. [swissprot;acc:p39026] Divided 241.828 267.346 1.10552
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Squared Subtracted 36933 44953.6 8020.6
deltex 2. [refseq;acc:nm_020892] Divided 6627.24 8484.19 1.2802
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Measured Subtracted 677.5 1865.5 1188
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Rooted Divided 57.9819 64.9302 1.11984
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Subtracted 108.659 100.356 8.303
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Measured Divided 5221.28 6314.35 1.20935
284 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Squared 59464 76120.8 1.28012
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Ranked 224.657 203.235 1.10541
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Rooted 51.8647 46.3161 1.1198
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Ranked Subtracted 242.686 265.516 22.83
paxillin. [swissprot;acc:p49023] Measured Divided 5221.28 6314.35 1.20935
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted 677.5 1865.5 1188
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Rooted 108.659 100.356 8.303
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Squared 36735.7 44689.6 7953.9
285 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Rooted Divided 48.4278 54.2262 1.11973
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Squared 6680.89 8549.44 1.27969
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked Subtracted 242.691 265.481 22.79
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Measured 4068.56 5252.6 1184.04
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Divided 23326.5 19296.4 1.20885
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Squared Subtracted 32117 40054 7937
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked Divided 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
286 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked 242.593 265.365 22.772
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] Divided 224.633 203.251 1.1052
exocyst complex component sec5. [swissprot;acc:q96kp1] Measured 23316 19288.8 1.20878
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared Subtracted 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
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked Divided 240.758 266.079 1.10517
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Measured Subtracted 4069.83 5252.17 1182.34
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Squared Divided 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
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 23303.1 19279.5 1.2087
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Ranked Subtracted 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
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared 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
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Measured 23422.4 19380.3 1.20857
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Squared 6693.64 8564.94 1.27956
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted 51.8789 46.3416 1.11949

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/