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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 325 to 374 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
41 GNAI3 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Measured Divided 1836.81 907.978 2.02297
Rooted 40.2797 24.3705 1.65281
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Squared 144912 81155 1.78562
TRO trophinin. [swissprot;acc:q12816] Measured Subtracted 23693.7 18263 5430.7
42 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 21785.2 16426.1 5359.1
jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 77.7233 16.8868
CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared 211446 137422 74024
FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked Divided 204.641 160.957 1.2714
GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Measured 1857.32 958.237 1.93827
Rooted 40.225 24.7051 1.62821
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared 144911 81154.7 1.78561
PBK 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] Ranked Subtracted 332.874 267.246 65.628
43 no value jun dimerization protein. [refseq;acc:nm_130469] Divided 204.641 160.957 1.2714
ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Measured Subtracted 21785.2 16426.1 5359.1
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared Divided 144876 81136.5 1.78558
FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Rooted Subtracted 60.8675 77.7168 16.8493
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Divided 40.6302 25.4452 1.59677
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Measured 1881.02 1027.36 1.83093
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked Subtracted 332.874 267.246 65.628
MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Squared 110342 184298 73956
44 DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured 28136.5 33457.6 5321.1
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 16.8473
FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Ranked Divided 204.641 161.046 1.2707
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 1.78117
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Measured 1931.34 1057.39 1.82652
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted 40.5691 25.4263 1.59556
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked Subtracted 332.874 267.246 65.628
MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Squared 110342 184298 73956
45 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 129597 73157.5 1.77148
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 110342 184298 73956
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked Divided 204.641 161.051 1.27066
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted Subtracted 60.875 77.7152 16.8402
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Divided 40.081 25.1546 1.59339
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1926.69 1056.02 1.82448
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Ranked Subtracted 332.874 267.246 65.628
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Measured 27642.5 22440.4 5202.1
46 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared Divided 129597 73157.5 1.77148
CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Measured Subtracted 24896.4 20431.7 4464.7
DTX2 deltex 2. [refseq;acc:nm_020892] Rooted Divided 27.634 43.9629 1.5909
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 161.068 1.27053
MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Rooted Subtracted 137.446 120.823 16.623
NEURL neuralized-like. [refseq;acc:nm_004210] Ranked 332.326 266.948 65.378
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured Divided 779.167 1390.33 1.78438
PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared Subtracted 210445 136779 73666
47 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 98517.9 56927.2 1.73059
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 779.167 1390.33 1.78438
DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 27.7078 44.017 1.58861
EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Squared Subtracted 210335 136716 73619
KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Measured 24896.4 20431.7 4464.7
MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Rooted 137.446 120.823 16.623

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
- Hugo is the HGNC identifier if it exists
- 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/