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 3858 to 3907 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
965 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Rooted 52.9804 50.0947 1.0576
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Ranked 211.987 204.964 1.03426
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Measured 11773.7 10733.8 1.09688
966 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Squared 22271.9 25656.8 1.15198
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Measured 7817.9 8575.12 1.09686
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Rooted 52.9804 50.0947 1.0576
tubby protein homolog. [swissprot;acc:p50607] Ranked 211.987 204.964 1.03426
967 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Squared 25580.6 29466.1 1.15189
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Measured 7813.35 8569.96 1.09684
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Ranked 211.987 204.964 1.03426
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Rooted 52.9804 50.0947 1.0576
968 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Squared 25580.6 29466.1 1.15189
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Ranked 211.987 204.964 1.03426
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Measured 7813.48 8570.11 1.09684
969 60s ribosomal protein l18. [swissprot;acc:q07020] Rooted 52.9804 50.0947 1.0576
band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] Measured 7813.34 8569.95 1.09684
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Squared 19488.7 22447.5 1.15182
tbc1 domain family member 5. [swissprot;acc:q92609] Ranked 211.987 204.964 1.03426
970 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Measured 7813.45 8570.07 1.09684
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Squared 24426.8 28125 1.1514
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Rooted 61.6649 65.1892 1.05715
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Ranked 211.987 204.964 1.03426
971 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Rooted 61.6649 65.1892 1.05715
acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] Squared 27478.1 31623.7 1.15087
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Measured 7813.36 8569.97 1.09684
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Ranked 211.987 204.964 1.03426
972 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Rooted 61.6649 65.1892 1.05715
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Measured 7813.48 8570.11 1.09684
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Ranked 211.987 204.964 1.03426
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Squared 21083.8 24262 1.15074
973 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Measured 7810.11 8566.29 1.09682
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Rooted 49.307 52.1123 1.05689
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Squared 27404 31534 1.15071
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Ranked 211.987 204.964 1.03426
974 delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] Squared 27403.4 31533.3 1.15071
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Measured 5365.06 5884.52 1.09682
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Rooted 61.8392 65.3085 1.0561
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Ranked 211.987 204.964 1.03426
975 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Measured 5365.14 5884.43 1.09679
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Squared 27403.4 31533.3 1.15071
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Ranked 211.987 204.964 1.03426
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Rooted 61.8392 65.3085 1.0561
976 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Measured 5365.22 5884.32 1.09675
lbp-9. [refseq;acc:nm_014553] Rooted 61.8392 65.3085 1.0561
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Squared 27403.7 31533.7 1.15071
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Ranked 243.34 235.322 1.03407
977 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 228.953 221.421 1.03402
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Rooted 61.8392 65.3085 1.0561
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Measured 4115.9 4513.14 1.09651

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/