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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1601 to 1650 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
Interaction Map
red
green
network_comparison
401 no value Divided sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Low confidence 205.017 197.863 1.03616
HTRA1 Subtracted serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 200.057 192.938 7.119
MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] High confidence 254.434 236.224 18.21
RPA1 Divided replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] 207.908 226.218 1.08807
402 CACNG5 Subtracted voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Low confidence 210.292 203.181 7.111
NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] High confidence 231.802 249.983 18.181
RPA2 Divided replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] 207.908 226.218 1.08807
TREX2 x-linked protein sts1769. [swissprot;acc:q99871] Low confidence 211.253 203.883 1.03615
403 ATRIP three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166]
HTRA3 Subtracted probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 200.049 192.942 7.107
MACF1 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] High confidence 228.468 246.338 17.87
PDC Divided phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 207.908 226.218 1.08807
404 DST Subtracted bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 228.463 246.33 17.867
GRM2 Divided metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Low confidence 203.081 196 1.03613
HTRA4 Subtracted probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 200.049 192.942 7.107
RAD52 Divided dna repair protein rad52 homolog. [swissprot;acc:p43351] High confidence 207.908 226.218 1.08807
405 no value metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Low confidence 203.081 196 1.03613
AP1G1 Subtracted adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] 207.442 200.339 7.103
CLTCL1 Divided clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] High confidence 207.931 226.209 1.0879
GABARAP Subtracted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 65.4586 83.0461 17.5875
406 no value Divided transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 265.634 244.304 1.08731
HTRA2 Subtracted serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Low confidence 200.046 192.943 7.103
LUC7L2 Divided luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 201.095 194.099 1.03604
NETO2 Subtracted neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] High confidence 237.109 254.667 17.558
407 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Low confidence 201.334 194.242 7.092
LUC7L Divided luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 201.123 194.127 1.03604
MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] High confidence 239.75 260.544 1.08673
NETO1 Subtracted neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 237.109 254.667 17.558
408 CEBPZ Divided ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 234.804 1.08649
GRM2 Subtracted metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Low confidence 203.081 196 7.081
HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] High confidence 237.109 254.667 17.558
JPH4 Divided adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Low confidence 207.558 200.363 1.03591
409 no value Subtracted metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 203.081 196 7.081
NFU1 Divided hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 149.423 144.256 1.03582
POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] High confidence 241.045 261.874 1.08641
RUNX2 Subtracted 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] 237.109 254.667 17.558
410 no value Divided tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 233.376 253.539 1.0864
ACTR3B Subtracted similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Low confidence 205.594 198.554 7.04
HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] High confidence 237.109 254.667 17.558
LSM4 Divided u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Low confidence 202.074 195.097 1.03576
411 C19orf29 Subtracted ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] 210.727 203.693 7.034
EGFL8 Divided palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 214.628 222.301 1.03575
GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] High confidence 233.376 253.539 1.0864
RPL18 Subtracted 60s ribosomal protein l18. [swissprot;acc:q07020] 237.109 254.667 17.558
412 LIMCH1 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Low confidence 210.594 203.561 7.033
NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] High confidence 251.926 234.547 17.379
SF3A2 Divided splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Low confidence 201.711 194.787 1.03555
UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] High confidence 240.788 261.416 1.08567
413 CACNG4 Subtracted voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Low confidence 210.252 203.24 7.012
KLF5 Divided krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] 201.711 194.787 1.03555

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/