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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expected Gene Rank measured Hugo description final
Results: HTML CSV LaTeX Showing element 2751 to 2800 of 3206 in total
expected
Rank
measured
Hugo
description
final
1.71846 1544 0.415555 NFKB1 NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT (DNA-BINDING FACTOR KBF1) (EBP- 1) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT]. [SWISSPROT;Acc:P19838] 0.241818256
1.71949 302 0.515003 ATG16L1 0.299509157
1.71958 1552 0.415409 EIF2B2 TRANSLATION INITIATION FACTOR EIF-2B BETA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR) (S20I15) (S20III15). [SWISSPROT;Acc:P49770] 0.24157585
1.72277 2731 0.354332 CRLS1 0.205675743
1.72628 850 0.449791 STAT5A SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 5A. [SWISSPROT;Acc:P42229] 0.260555066
1.7269 1674 0.41158 PSMD10 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10 (26S PROTEASOME REGULATORY SUBUNIT P28) (GANKYRIN). [SWISSPROT;Acc:O75832] 0.238334588
1.73336 1896 0.403209 VPS39 VAM6/VPS39-LIKE PROTEIN (HVAM6P). [SWISSPROT;Acc:Q96JC1] 0.232616998
1.73399 646 0.464913 RANBP2 RAN-BINDING PROTEIN 2 (RANBP2) (NUCLEAR PORE COMPLEX PROTEIN NUP358) (NUCLEOPORIN NUP358) (358 KDA NUCLEOPORIN) (P270). [SWISSPROT;Acc:P49792] 0.268117463
1.738 2988 0.240182 ARRB2 "BETA-ARRESTIN 2 (ARRESTIN, BETA 2). [SWISSPROT;Acc:P32121]" 0.138194476
1.74133 1689 0.414602 GAPDH "GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, LIVER (EC 1.2.1.12) (GAPDH). [SWISSPROT;Acc:P04406]" 0.238095019
1.74487 1965 0.403445 CMPK UMP-CMP KINASE (EC 2.7.4.14) (CYTIDYLATE KINASE) (DEOXYCYTIDYLATE KINASE) (CYTIDINE MONOPHOSPHATE KINASE). [SWISSPROT;Acc:P30085] 0.231217798
1.74675 1383 0.427194 UBQLN4 ATAXIN-1 UBIQUITIN-LIKE INTERACTING PROTEIN. [RefSeq;Acc:NM_020131] 0.244565049
1.74914 3083 0.174683 HOMER2 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 2; HOMER HOMOLOG 3 (DROSOPHILA). [RefSeq;Acc:NM_004839]" 0.099867935
1.75288 240 0.547661 PRKAA1 "5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-1 CHAIN (EC 2.7.1.-) (AMPK ALPHA-1 CHAIN). [SWISSPROT;Acc:Q13131]" 0.312434964
1.75491 1545 0.424367 BCL3 B-CELL LYMPHOMA 3-ENCODED PROTEIN (BCL-3 PROTEIN). [SWISSPROT;Acc:P20749] 0.241816959
1.75758 2164 0.399289 PSMD2 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 2 (26S PROTEASOME REGULATORY SUBUNIT S2) (26S PROTEASOME SUBUNIT P97) (TUMOR NECROSIS FACTOR TYPE 1 RECEPTOR ASSOCIATED PROTEIN 2) (55.11 PROTEIN). [SWISSPROT;Acc:Q13200] 0.227181124
1.76144 1973 0.407104 RAD51 DNA REPAIR PROTEIN RAD51 HOMOLOG 1 (HRAD51) (HSRAD51). [SWISSPROT;Acc:Q06609] 0.231119993
1.76198 473 0.483455 FOXA3 HEPATOCYTE NUCLEAR FACTOR 3-GAMMA (HNF-3G) (FORKHEAD BOX PROTEIN A3) (FORK HEAD-RELATED PROTEIN FKH H3). [SWISSPROT;Acc:P55318] 0.274381662
1.7666 643 0.473678 SUMO1P3 UBIQUITIN-LIKE PROTEIN SMT3C PRECURSOR (UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1) (UBIQUITIN-LIKE PROTEIN UBL1) (UBIQUITIN-RELATED PROTEIN SUMO-1) (GAP MODIFYING PROTEIN 1) (GMP1) (SENTRIN). [SWISSPROT;Acc:Q93068] 0.268129741
1.77067 319 0.515195 PRPF31 PRE-MRNA PROCESSING FACTOR 31 HOMOLOG; PRE-MRNA PROCESSING FACTOR 31 HOMOLOG (YEAST). [RefSeq;Acc:NM_015629] 0.290960484
1.77366 2466 0.384329 LGALS4 GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [SWISSPROT;Acc:P56470] 0.216686964
1.77434 2348 0.391086 TAF6 TRANSCRIPTION INITIATION FACTOR TFIID 70 KDA SUBUNIT (TAFII-70) (TAFII-80) (TAFII80). [SWISSPROT;Acc:P49848] 0.220412097
1.77451 2111 0.405058 STAM SIGNAL TRANSDUCING ADAPTOR MOLECULE 1; SIGNAL TRANSDUCING ADAPTOR MOLECULE. [RefSeq;Acc:NM_003473] 0.228264704
1.77482 1757 0.420128 ATP6V1E2 0.236715836
1.77573 3182 0.0883895 FBXW7 "F-BOX PROTEIN FBW7 ISOFORM 2; ARCHIPELAGO, DROSOPHILA, HOMOLOG OF; F-BOX PROTEIN FBW7; F-BOX PROTEIN SEL-10; HOMOLOG OF C ELEGANS SEL-10. [RefSeq;Acc:NM_018315]" 0.04977643
1.77667 279 0.539996 NCK1 CYTOPLASMIC PROTEIN NCK1 (NCK ADAPTOR PROTEIN 1) (SH2/SH3 ADAPTOR PROTEIN NCK-ALPHA). [SWISSPROT;Acc:P16333] 0.303937141
1.77681 849 0.462971 STAT5B SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 5B. [SWISSPROT;Acc:P51692] 0.260563032
1.77759 2741 0.364089 CPSF4 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 4, 30KD SUBUNIT; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR, 30KD; NO ARCHES-LIKE (ZEBRAFISH) ZINC FINGER PROTEIN; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR. [RefSeq;Acc:NM_006693]" 0.204821697
1.77935 1903 0.413255 SHMT2 "SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34897]" 0.232250541
1.78008 3063 0.18745 GNB4 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 4 (TRANSDUCIN BETA CHAIN 4). [SWISSPROT;Acc:Q9HAV0] 0.105304256
1.78081 3130 0.121984 MYO5C MYOSIN VC (MYOSIN 5C). [SWISSPROT;Acc:Q9NQX4] 0.068499166
1.78321 2299 0.396471 TAF12 TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS (TAFII- 20/TAFII-15) (TAFII20/TAFII15). [SWISSPROT;Acc:Q16514] 0.222335563
1.78381 3203 0.0426192 RRAGB RAS-RELATED GTP BINDING B SHORT ISOFORM; GTP-BINDING PROTEIN RAGB. [RefSeq;Acc:NM_006064] 0.023892231
1.78474 2740 0.366149 CPSF2 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KDA SUBUNIT (CPSF 100 KDA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q9P2I0]" 0.205155373
1.78896 579 0.483254 C14orf4 0.270131249
1.78993 1898 0.416108 MTIF2 "TRANSLATION INITIATION FACTOR IF-2, MITOCHONDRIAL PRECURSOR (IF-2MT) (IF-2(MT)). [SWISSPROT;Acc:P46199]" 0.232471661
1.79234 2562 0.383439 ATP5A1 "ATP SYNTHASE ALPHA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P25705]" 0.213932066
1.79432 1760 0.424679 ATP6V1F VACUOLAR ATP SYNTHASE SUBUNIT F (EC 3.6.3.14) (V-ATPASE F SUBUNIT) (VACUOLAR PROTON PUMP F SUBUNIT) (V-ATPASE 14 KDA SUBUNIT). [SWISSPROT;Acc:Q16864] 0.236679634
1.79509 2074 0.411592 no value SIGNAL RECOGNITION PARTICLE RECEPTOR ALPHA SUBUNIT (SR-ALPHA) (DOCKING PROTEIN ALPHA) (DP-ALPHA). [SWISSPROT;Acc:P08240] 0.229287668
1.80704 2921 0.304269 PNAS-18. [SPTREMBL;Acc:Q9BZU3] 0.168379781
1.80836 2829 0.349731 DPM1 DOLICHOL-PHOSPHATE MANNOSYLTRANSFERASE (EC 2.4.1.83) (DOLICHOL- PHOSPHATE MANNOSE SYNTHASE) (DOLICHYL-PHOSPHATE BETA-D- MANNOSYLTRANSFERASE) (MANNOSE-P-DOLICHOL SYNTHASE) (MPD SYNTHASE) (DPM SYNTHASE). [SWISSPROT;Acc:O60762] 0.193396779
1.81111 2680 0.377523 PAPOLG POLY(A) POLYMERASE GAMMA (EC 2.7.7.19) (PAP GAMMA) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE GAMMA) (SRP RNA 3' ADENYLATING ENZYME). [SWISSPROT;Acc:Q9BWT3] 0.20844841
1.82552 1316 0.448528 no value TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [RefSeq;Acc:NM_014886] 0.24569876
1.82907 1962 0.422914 AK3 GTP:AMP PHOSPHOTRANSFERASE MITOCHONDRIAL (EC 2.7.4.10) (AK3) (ADENYLATE KINASE 3 ALPHA LIKE 1). [SWISSPROT;Acc:Q9UIJ7] 0.231218051
1.82999 275 0.557721 SF3B2 SPLICING FACTOR 3B SUBUNIT 2 (SPLICEOSOME ASSOCIATED PROTEIN 145) (SAP 145) (SF3B150) (PRE-MRNA SPLICING FACTOR SF3B 145 KDA SUBUNIT). [SWISSPROT;Acc:Q13435] 0.304767239
1.83073 572 0.495507 ELAVL4 ELAV-LIKE PROTEIN 4 (PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD) (HU-ANTIGEN D). [SWISSPROT;Acc:P26378] 0.270660884
1.83168 574 0.495602 ELAVL2 ELAV-LIKE PROTEIN 2 (HU-ANTIGEN B) (HUB) (ELAV-LIKE NEURONAL PROTEIN 1) (NERVOUS SYSTEM-SPECIFIC RNA BINDING PROTEIN HEL-N1). [SWISSPROT;Acc:Q12926] 0.270572371
1.83532 2675 0.383112 TAF9B "TBP-ASSOCIATED FACTOR 9L; NEURONAL CELL DEATH-RELATED PROTEIN; TAF9-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 31 KD; NEURONAL CELL DEATH-RELATED GENE IN NEURON-7; TRANSCRIPTION ASSOCIATED FACTOR TAFII31L; TRANSCRIPTION INIT" 0.208743979
1.8374 2779 0.369521 ISL2 INSULIN GENE ENHANCER PROTEIN ISL-2 (ISLET-2). [SWISSPROT;Acc:Q96A47] 0.201110809
1.84052 848 0.479679 SFRS18 SR RICH PROTEIN. [RefSeq;Acc:NM_032870] 0.260621455

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/