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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1075 to 1124 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
269 PCYT1A 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] 241.373 267.352 1.10763
SLC46A2 Squared thymic stromal co-transporter. [refseq;acc:nm_033051] 26157.6 20236.2 1.29261
270 C16orf80 transcription factor iib. [refseq;acc:nm_013242] 64739.9 50300.6 1.28706
CRKL Rooted crk-like protein. [swissprot;acc:p46109] 66.1064 74.1074 1.12103
FIP1L1 Measured fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 23640.2 19479.8 1.21358
FLAD1 Ranked fad synthetase. [refseq;acc:nm_025207] 241.373 267.352 1.10763
271 no value 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]
ABL1 Rooted proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 66.1064 74.1073 1.12103
CHRAC1 Measured chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 2554.89 3093.78 1.21092
SFRS8 Squared splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] 64739.9 50300.6 1.28706
272 FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 36563.7 46971.1 1.28464
FYN Rooted proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 66.1064 74.1074 1.12103
HAT1 Measured histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 3858.52 4669.27 1.21012
LGTN Ranked ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 241.373 267.352 1.10763
273 EIF5 Measured eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 3199.4 3870.8 1.20985
FGR Rooted proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 66.1064 74.1074 1.12103
FLNB 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 20665.7 1.28198
PAPSS1 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] 241.373 267.352 1.10763
274 GRAP2 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 74.1068 1.12102
POR Ranked nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 241.373 267.352 1.10763
RBM15B Measured chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 3119.98 2579.49 1.20953
REV1 Squared rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 16120.1 20665.7 1.28198
275 CUTL1 Rooted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 66.1048 74.0977 1.12091
PCYT1B 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] 241.373 267.352 1.10763
PRMT1 Squared protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 16120.1 20665.7 1.28198
RGS19 Measured regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 3119.98 2579.49 1.20953
276 CUTL2 Rooted homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 66.1046 74.0964 1.1209
PRMT8 Squared protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 16120.1 20665.7 1.28198
RBM15 Measured putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 3119.98 2579.49 1.20953
SNORA7A Ranked 60s ribosomal protein l32. [swissprot;acc:p02433] 241.13 266.969 1.10716
277 no value 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 267.642 1.10665
RGS20 Measured regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] 3119.98 2579.49 1.20953
RPS6KC1 Rooted ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 65.9938 73.9449 1.12048
SNRP70 Squared u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 16120.1 20665.7 1.28198
278 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
Rooted ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 65.9938 73.9449 1.12048
LBX1 Measured transcription factor lbx1. [swissprot;acc:p52954] 3119.98 2579.49 1.20953
RPS11 Ranked 40s ribosomal protein s11. [swissprot;acc:p04643] 241.399 267.088 1.10642
279 GPSM2 Measured mosaic protein lgn. [swissprot;acc:p81274] 3119.98 2579.49 1.20953
MSI2 Squared musashi 2 isoform a. [refseq;acc:nm_138962] 15569.5 19953.6 1.28158
RBBP7 Ranked histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 252.644 228.42 1.10605
WASL Rooted neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 66.0989 74.0609 1.12046
280 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 57.9068 64.8562 1.12001
MSI1 Squared musashi 1. [refseq;acc:nm_002442] 15569.5 19953.6 1.28158
MTA1 Ranked metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 228.356 1.10578
RGS17 Measured regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 3119.98 2579.49 1.20953
281 no value Ranked 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 1.10557
GNAO1 Measured guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 3119.98 2579.49 1.20953
SNRPA1 Rooted u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 57.9068 64.8562 1.12001
ZC3H14 Squared nuclear protein ukp68. [refseq;acc:nm_024824] 15569.5 19953.6 1.28158

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/