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 Value Type description Interaction Map Network Comparison Type Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 12912 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
Rank
Value Type
description
red
network_comparison
green
263 Squared adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 26157.6 1.29261 20236.2
Rooted paxillin. [swissprot;acc:p49023] 59.4073 1.12276 66.7002
264 Measured cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4987.58 1.2181 4094.57
Ranked mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 219.421 1.11394 196.978
Squared adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 26157.6 1.29261 20236.2
Rooted wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 66.1122 1.12148 74.1438
265 Measured wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 24806.9 1.21782 20369.9
Ranked splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 225.217 1.11241 202.459
Squared leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 26157.6 1.29261 20236.2
Rooted u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 56.031 1.12131 62.8281
266 Measured cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 24806.9 1.21782 20369.9
Ranked transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 241.07 1.11121 267.88
Squared fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 26157.6 1.29261 20236.2
Rooted proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 66.1064 1.12103 74.1074
267 Measured ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 14021.4 1.21682 11523
Ranked density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 241.07 1.11121 267.88
Squared leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 26157.6 1.29261 20236.2
Rooted tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 66.1064 1.12103 74.1073
268 Measured cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 24473.9 1.21593 20127.8
Ranked eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 271.016 1.10996 244.167
Squared laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 26157.6 1.29261 20236.2
Rooted proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 66.1064 1.12103 74.1074
269 Measured u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 4590.18 1.21466 5575.52
Ranked cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 241.373 1.10763 267.352
Squared thymic stromal co-transporter. [refseq;acc:nm_033051] 26157.6 1.29261 20236.2
Rooted tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 66.1064 1.12103 74.1074
270 Measured fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 23640.2 1.21358 19479.8
Ranked fad synthetase. [refseq;acc:nm_025207] 241.373 1.10763 267.352
Squared transcription factor iib. [refseq;acc:nm_013242] 64739.9 1.28706 50300.6
Rooted crk-like protein. [swissprot;acc:p46109] 66.1064 1.12103 74.1074
271 Measured chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 2554.89 1.21092 3093.78
Ranked 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] 241.373 1.10763 267.352
Squared splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] 64739.9 1.28706 50300.6
Rooted proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 66.1064 1.12103 74.1073
272 Measured histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 3858.52 1.21012 4669.27
Ranked ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 241.373 1.10763 267.352
Squared adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 36563.7 1.28464 46971.1
Rooted proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 66.1064 1.12103 74.1074
273 Measured eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 3199.4 1.20985 3870.8
Ranked 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] 241.373 1.10763 267.352
Squared 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] 16120.1 1.28198 20665.7
Rooted proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 66.1064 1.12103 74.1074
274 Measured chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 3119.98 1.20953 2579.49
Ranked nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 241.373 1.10763 267.352
Squared rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 16120.1 1.28198 20665.7
Rooted 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] 66.1063 1.12102 74.1068
275 Measured regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 3119.98 1.20953 2579.49
Ranked cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 241.373 1.10763 267.352
Squared protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 16120.1 1.28198 20665.7
Rooted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 66.1048 1.12091 74.0977

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/