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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
Rank
description
measured
expected
final
Hugo
1 PROTEIN CGI-126 (PROTEIN HSPC155). [SWISSPROT;Acc:Q9Y3C8] 0.790808 0.682179 1.159238264 UFC1
2 RAD50-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_021930] 1.28125 1.1674 1.097524413 RINT1
3 RHO-RELATED BTB DOMAIN-CONTAINING PROTEIN 2 (DELETED IN BREAST CANCER 2 GENE PROTEIN) (P83). [SWISSPROT;Acc:Q9BYZ6] RHOBTB2
4 3.66001 3.3348 1.097520091 no value
5 "NADH-UBIQUINONE OXIDOREDUCTASE 18 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-18 KDA) (CI-18 KDA) (COMPLEX I- AQDQ) (CI-AQDQ). [SWISSPROT;Acc:O43181]" 0.489705 0.74385 0.658338375 NDUFS4
6 CHROMATIN ACCESSIBILITY COMPLEX PROTEIN 1 (CHRAC-1) (CHRAC-15) (HUCHRAC15) (DNA POLYMERASE EPSILON SUBUNIT P15). [SWISSPROT;Acc:Q9NRG0] 0.590586 0.969328 0.609273641 CHRAC1
7 ADIPONECTIN RECEPTOR 2. [RefSeq;Acc:NM_024551] 0.252763 0.428531 0.589835975 ADIPOR2
8 ODD-SKIPPED RELATED 1; ODZ (ODD OZ/TEN-M) RELATED 1. [RefSeq;Acc:NM_145260] 0.281519 0.487701 0.577236873 OSR1
9 DNA POLYMERASE EPSILON P12 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 4). [SWISSPROT;Acc:Q9NR33] 0.803534 1.40271 0.572843995 POLE4
10 PROTEIN X 0004. [RefSeq;Acc:NM_016301] 0.271296 0.5 0.542592 ATPBD1C
11 XPA BINDING PROTEIN 1; MBD2 INTERACTOR PROTEIN; PUTATIVE ATP(GTP)-BINDING PROTEIN. [RefSeq;Acc:NM_007266] 0.813888 1.5 XAB1
12 HBS1-LIKE. [RefSeq;Acc:NM_006620] 0.250879 0.5 0.501758 HBS1L
13 HOMEOBOX PROTEIN HLX1 (HOMEOBOX PROTEIN HB24). [SWISSPROT;Acc:Q14774] HLX
14 NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA (NF-Y PROTEIN CHAIN B) (NF-YB) (CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT A) (CBF-A) (CAAT- BOX DNA BINDING PROTEIN SUBUNIT B). [SWISSPROT;Acc:P25208] 0.439158 0.912166 0.481445263 NFYB
15 GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 (GRB2 ADAPTER PROTEIN) (SH2/SH3 ADAPTER GRB2) (ASH PROTEIN). [SWISSPROT;Acc:P29354] 1.95189 4.10415 0.475589342 GRB2
16 SERINE/THREONINE-PROTEIN KINASE NEK2 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 2) (NIMA-LIKE PROTEIN KINASE 1) (HSPK 21). [SWISSPROT;Acc:P51955] 0.106175 0.22325 0.475587906 NEK2
17 0.0856348 0.180231 0.475139127 no value
18 0.0773877 0.162874 0.475138451 FAM49B
19 E2A-PBX1-ASSOCIATED PROTEIN; PUTATIVE 47 KDA PROTEIN. [RefSeq;Acc:NM_020140] 0.310118 0.652691 0.475137546 ANKS1B
20 NEURON NAVIGATOR 1; NEURON NAVIGATOR-1; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 3. [RefSeq;Acc:NM_020443] 0.149206 0.314027 0.475137488 NAV1
21 NEURON NAVIGATOR 3; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 1; STEERIN 3. [RefSeq;Acc:NM_014903] 0.150125 0.315963 0.475134747 NAV3
22 NEURON NAVIGATOR 2 ISOFORM L; RETINOIC ACID INDUCIBLE IN NEUROBLASTOMA; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 2; HELICASE HELAD1. [RefSeq;Acc:NM_145117] 0.192159 0.404444 0.475118929 NAV2
23 GRB2-RELATED ADAPTOR PROTEIN. [SWISSPROT;Acc:Q13588] 1.4649 3.08715 0.47451533 GRAP
24 0.229891 0.5 0.459782 CNOT10
25 DNA-REPAIR PROTEIN COMPLEMENTING XP-G CELLS (XERODERMA PIGMENTOSUM GROUP G COMPLEMENTING PROTEIN) (DNA EXCISION REPAIR PROTEIN ERCC-5). [SWISSPROT;Acc:P28715] 0.364125 0.853699 0.426526211 ERCC5
26 DOCKING PROTEIN 2 (P56(DOK-2)) (DOWNSTREAM OF TYROSINE KINASE 2). [SWISSPROT;Acc:O60496] 0.0954445 0.223986 0.42611815 DOK2
27 TYROSINE-PROTEIN KINASE FRK (EC 2.7.1.112) (NUCLEAR TYROSINE PROTEIN KINASE RAK). [SWISSPROT;Acc:P42685] 0.643425 1.50997 0.426117737 FRK
28 DOK-LIKE PROTEIN. [RefSeq;Acc:NM_024872] 0.0753031 0.176719 0.426117735 no value
29 DOCKING PROTEIN 1 (P62(DOK)) (DOWNSTREAM OF TYROSINE KINASE 1) (PP62). [SWISSPROT;Acc:Q99704] 0.0754466 0.177056 0.426117161 DOK1
30 TATA-BINDING PROTEIN-ASSOCIATED PHOSPHOPROTEIN (DOWN-REGULATOR OF TRANSCRIPTION 1) (DR1 PROTEIN). [SWISSPROT;Acc:Q01658] 0.263027 0.621928 0.422921946 DR1
31 WISKOTT-ALDRICH SYNDROME PROTEIN (WASP). [SWISSPROT;Acc:P42768] 1.97356 4.68345 0.421390214 WAS
32 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC) (C-SRC). [SWISSPROT;Acc:P12931] 0.141847 0.33698 0.420935961 no value
33 TYROSINE-PROTEIN KINASE HCK (EC 2.7.1.112) (P59-HCK/P60-HCK) (HEMOPOIETIC CELL KINASE). [SWISSPROT;Acc:P08631] HCK
34 PROTO-ONCOGENE C-CRK (P38) (ADAPTER MOLECULE CRK). [SWISSPROT;Acc:P46108] 0.142264 0.337971 0.420935524 CRK
35 CRK-LIKE PROTEIN. [SWISSPROT;Acc:P46109] 0.142003 0.337351 0.420935465 CRKL
36 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1 (EC 2.7.1.112) (P150) (C-ABL). [SWISSPROT;Acc:P00519] 0.143775 0.341561 0.42093506 ABL1
37 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FGR (EC 2.7.1.112) (P55-FGR) (C-FGR). [SWISSPROT;Acc:P09769] 0.14242 0.338342 0.42093503 FGR
38 TYROSINE-PROTEIN KINASE ABL2 (EC 2.7.1.112) (TYROSINE KINASE ARG). [SWISSPROT;Acc:P42684] 0.143514 0.340942 0.420933766 ABL2
39 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN (EC 2.7.1.112) (P59-FYN) (SYN) (SLK). [SWISSPROT;Acc:P06241] 0.14268 0.338961 0.420933382 FYN
40 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- 0.160294 0.380812 0.420926862 GRAP2
41 CCAAT DISPLACEMENT PROTEIN (CDP) (CUT-LIKE 1). [SWISSPROT;Acc:P39880] 0.187173 0.444789 0.420813015 CUTL1
42 HOMEOBOX PROTEIN CUX-2 (CUT-LIKE 2) (FRAGMENT). [SWISSPROT;Acc:O14529] 0.147881 0.35143 0.420797883 CUTL2
43 NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN (N-WASP). [SWISSPROT;Acc:O00401] 1.66627 3.96399 0.420351716 WASL
44 HEPATOCYTE NUCLEAR FACTOR 4-ALPHA (HNF-4-ALPHA) (TRANSCRIPTION FACTOR HNF-4) (TRANSCRIPTION FACTOR 14). [SWISSPROT;Acc:P41235] 0.144656 0.346879 0.417021497 HNF4A
45 GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA (CYTOKINE RESPONSIVE PROTEIN CR6). [SWISSPROT;Acc:O95257] 0.203633 0.488304 0.417020954 GADD45G
46 HEPATOCYTE NUCLEAR FACTOR 4-GAMMA (HNF-4-GAMMA). [SWISSPROT;Acc:Q14541] 0.117156 0.280936 0.417020247 HNF4G
47 GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 BETA (NEGATIVE GROWTH-REGULATORY PROTEIN MYD118) (MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD118). [SWISSPROT;Acc:O75293] 0.173246 0.415438 0.417020109 GADD45B
48 GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 ALPHA (DNA- DAMAGE INDUCIBLE TRANSCRIPT 1) (DDIT1). [SWISSPROT;Acc:P24522] 0.174044 0.417352 0.417019686 GADD45A
49 FERRITIN HEAVY CHAIN (FERRITIN H SUBUNIT). [SWISSPROT;Acc:P02794] 0.788413 1.91686 0.411304425 FTH1
50 FERRITIN LIGHT CHAIN (FERRITIN L SUBUNIT). [SWISSPROT;Acc:P02792] 0.0515298 0.125329 0.411156237 FTL

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/