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 2110 to 2159 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
264 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked Divided 219.421 196.978 1.11394
ns1-associated protein 1. [refseq;acc:nm_006372] Rooted Subtracted 52.7642 61.9019 9.1377
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Divided 66.1122 74.1438 1.12148
265 60s ribosomal protein l9. [swissprot;acc:p32969] Ranked Subtracted 240.243 263.798 23.555
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Squared 53174 44377.4 8796.6
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Rooted 52.7642 61.9019 9.1377
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Squared Divided 26157.6 20236.2 1.29261
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Measured Subtracted 4638.1 5923.4 1285.3
Ranked Divided 225.217 202.459 1.11241
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 56.031 62.8281 1.12131
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 20369.9 1.21782
266 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Rooted Subtracted 52.7702 61.8915 9.1213
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Squared Divided 26157.6 20236.2 1.29261
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Subtracted 59335 68062.6 8727.6
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted Divided 66.1064 74.1074 1.12103
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Ranked Subtracted 243.12 266.662 23.542
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Measured 11222.2 9948.93 1273.27
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked Divided 241.07 267.88 1.11121
267 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Subtracted 243.12 266.661 23.541
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Measured 11222.2 9948.93 1273.27
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Ranked Divided 241.07 267.88 1.11121
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Squared Subtracted 59334.6 68040.1 8705.5
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Divided 26157.6 20236.2 1.29261
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 14021.4 11523 1.21682
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted Subtracted 61.2893 70.3856 9.0963
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Divided 66.1064 74.1073 1.12103
268 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Measured Subtracted 11222.2 9948.93 1273.27
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided 24473.9 20127.8 1.21593
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked 271.016 244.167 1.10996
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Squared 26157.6 20236.2 1.29261
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted Subtracted 61.2893 70.3856 9.0963
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Ranked 241.625 265.136 23.511
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted Divided 66.1064 74.1074 1.12103
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Squared Subtracted 35533.9 44227 8693.1
269 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Ranked 241.625 265.136 23.511
armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Squared 35508.7 44191.4 8682.7
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Ranked Divided 241.373 267.352 1.10763
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Measured Subtracted 4808.79 6074.21 1265.42
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Rooted 61.2893 70.3856 9.0963
thymic stromal co-transporter. [refseq;acc:nm_033051] Squared Divided 26157.6 20236.2 1.29261
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Rooted 66.1064 74.1074 1.12103
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured 4590.18 5575.52 1.21466
270 40s ribosomal protein s3. [swissprot;acc:p23396] Ranked Subtracted 241.612 265.119 23.507
crk-like protein. [swissprot;acc:p46109] Rooted Divided 66.1064 74.1074 1.12103
fad synthetase. [refseq;acc:nm_025207] Ranked 241.373 267.352 1.10763
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 19479.8 1.21358
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Squared Subtracted 35508.6 44191.3 8682.7
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured 4810.22 6075.04 1264.82
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 39.0445 9.007

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/