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 green red network_comparison
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
green
red
network_comparison
263 paxillin. [swissprot;acc:p49023] Rooted 66.7002 59.4073 1.12276
trs85 homolog. [swissprot;acc:q9y2l5] Measured 20431.7 24896.4 1.21852
264 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Squared 20236.2 26157.6 1.29261
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured 4094.57 4987.58 1.2181
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked 196.978 219.421 1.11394
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Rooted 74.1438 66.1122 1.12148
265 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Squared 20236.2 26157.6 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] Ranked 202.459 225.217 1.11241
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 62.8281 56.031 1.12131
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 20369.9 24806.9 1.21782
266 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Squared 20236.2 26157.6 1.29261
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted 74.1074 66.1064 1.12103
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked 267.88 241.07 1.11121
267 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Squared 20236.2 26157.6 1.29261
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 11523 14021.4 1.21682
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted 74.1073 66.1064 1.12103
268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Measured 20127.8 24473.9 1.21593
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked 244.167 271.016 1.10996
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Squared 20236.2 26157.6 1.29261
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 74.1074 66.1064 1.12103
269 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 267.352 241.373 1.10763
thymic stromal co-transporter. [refseq;acc:nm_033051] Squared 20236.2 26157.6 1.29261
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Rooted 74.1074 66.1064 1.12103
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured 5575.52 4590.18 1.21466
270 crk-like protein. [swissprot;acc:p46109] Rooted 74.1074 66.1064 1.12103
fad synthetase. [refseq;acc:nm_025207] Ranked 267.352 241.373 1.10763
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 19479.8 23640.2 1.21358
transcription factor iib. [refseq;acc:nm_013242] Squared 50300.6 64739.9 1.28706
271 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked 267.352 241.373 1.10763
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Measured 3093.78 2554.89 1.21092
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Rooted 74.1073 66.1064 1.12103
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Squared 50300.6 64739.9 1.28706
272 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 46971.1 36563.7 1.28464
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Measured 4669.27 3858.52 1.21012
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked 267.352 241.373 1.10763
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted 74.1074 66.1064 1.12103
273 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Ranked 267.352 241.373 1.10763
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured 3870.8 3199.4 1.20985
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Squared 20665.7 16120.1 1.28198
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Rooted 74.1074 66.1064 1.12103
274 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Measured 2579.49 3119.98 1.20953
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Rooted 74.1068 66.1063 1.12102
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Ranked 267.352 241.373 1.10763
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Squared 20665.7 16120.1 1.28198
275 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Rooted 74.0977 66.1048 1.12091
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Ranked 267.352 241.373 1.10763
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Squared 20665.7 16120.1 1.28198
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Measured 2579.49 3119.98 1.20953

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/