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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measured Gene Rank Hugo description expected final
Results: HTML CSV LaTeX Showing element 2758 to 2807 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.41158 1674 PSMD10 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10 (26S PROTEASOME REGULATORY SUBUNIT P28) (GANKYRIN). [SWISSPROT;Acc:O75832] 1.7269 0.238334588
0.411592 2074 no value SIGNAL RECOGNITION PARTICLE RECEPTOR ALPHA SUBUNIT (SR-ALPHA) (DOCKING PROTEIN ALPHA) (DP-ALPHA). [SWISSPROT;Acc:P08240] 1.79509 0.229287668
0.412088 2704 CPSF3 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 73 KDA SUBUNIT (CPSF 73 KDA SUBUNIT). [SWISSPROT;Acc:Q9UKF6]" 1.98586 0.207511104
0.412171 2618 CSTF3 "CLEAVAGE STIMULATION FACTOR SUBUNIT 3; CLEAVAGE STIMULATION FACTOR, 3' PRE-RNA, SUBUNIT 3, 77KD. [RefSeq;Acc:NM_001326]" 1.95716 0.210596477
0.412942 1070 GMCL1 1.63455 0.252633447
0.413255 1903 SHMT2 "SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34897]" 1.77935 0.232250541
0.414022 596 FOXA2 HEPATOCYTE NUCLEAR FACTOR 3-BETA (HNF-3B) (FORKHEAD BOX PROTEIN A2). [SWISSPROT;Acc:Q9Y261] 1.53743 0.269294862
0.414602 1689 GAPDH "GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, LIVER (EC 1.2.1.12) (GAPDH). [SWISSPROT;Acc:P04406]" 1.74133 0.238095019
0.414708 1543 NFKBIB NF-KAPPAB INHIBITOR BETA (NF-KAPPA-BIB) (I-KAPPA-B-BETA) (IKAPPABBETA) (IKB-BETA) (IKB-B) (THYROID RECEPTOR INTERACTING PROTEIN 9) (TR- INTERACTING PROTEIN 9). [SWISSPROT;Acc:Q15653] 1.71495 0.241819295
0.415216 1542 NFKB2 NUCLEAR FACTOR NF-KAPPA-B P100/P49 SUBUNITS (H2TF1) (ONCOGENE LYT-10) (LYT10) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P52 SUBUNIT]. [SWISSPROT;Acc:Q00653] 1.71705 0.2418194
0.415409 1552 EIF2B2 TRANSLATION INITIATION FACTOR EIF-2B BETA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR) (S20I15) (S20III15). [SWISSPROT;Acc:P49770] 1.71958 0.24157585
0.415555 1544 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] 1.71846 0.241818256
0.416108 1898 MTIF2 "TRANSLATION INITIATION FACTOR IF-2, MITOCHONDRIAL PRECURSOR (IF-2MT) (IF-2(MT)). [SWISSPROT;Acc:P46199]" 1.78993 0.232471661
0.416194 2717 SLC27A4 "SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 4; FATTY ACID TRANSPORT PROTEIN 4. [RefSeq;Acc:NM_005094]" 2.00736 0.207334011
0.416438 2634 ISCU NITROGEN FIXATION CLUSTER-LIKE. [RefSeq;Acc:NM_014301] 1.98305 0.209998739
0.416665 258 EIF3B EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 9 (EIF-3 ETA) (EIF3 P116) (EIF3 P110) (EIF3B). [SWISSPROT;Acc:P55884] 1.3435 0.310133978
0.418445 833 KHSRP KH-TYPE SPLICING REGULATORY PROTEIN (FUSE BINDING PROTEIN 2); KH-TYPE SPLICING REGULATORY PROTEIN (FUSE-BINDING PROTEIN 2). [RefSeq;Acc:NM_003685] 1.60336 0.260980067
0.419259 266 EIF3C EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 8 (EIF3 P110) (EIF3C). [SWISSPROT;Acc:Q99613] 1.36159 0.307918683
0.419455 921 STUB1 STIP1 HOMOLOGY AND U-BOX CONTAINING PROTEIN 1; SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 7; CARBOXY TERMINUS OF HSP70P-INTERACTING PROTEIN; HEAT SHOCK PROTEIN A BINDING PROTEIN 2 (C-TERMINAL). [RefSeq;Acc:NM_005861] 1.6262 0.257935678
0.420128 1757 ATP6V1E2 1.77482 0.236715836
0.42132 2464 TADA2L TRANSCRIPTIONAL ADAPTER 2-LIKE (ADA2-LIKE PROTEIN) (KL04P). [SWISSPROT;Acc:O75478] 1.94413 0.216713903
0.42248 2227 FDX1 "ADRENODOXIN, MITOCHONDRIAL PRECURSOR (ADRENAL FERREDOXIN) (HEPATOREDOXIN) (FERREDOXIN 1). [SWISSPROT;Acc:P10109]" 1.8831 0.22435346
0.422914 1962 AK3 GTP:AMP PHOSPHOTRANSFERASE MITOCHONDRIAL (EC 2.7.4.10) (AK3) (ADENYLATE KINASE 3 ALPHA LIKE 1). [SWISSPROT;Acc:Q9UIJ7] 1.82907 0.231218051
0.424367 1545 BCL3 B-CELL LYMPHOMA 3-ENCODED PROTEIN (BCL-3 PROTEIN). [SWISSPROT;Acc:P20749] 1.75491 0.241816959
0.424547 514 RBM9 RNA-BINDING PROTEIN 9 (RNA BINDING MOTIF PROTEIN 9) (HEXARIBONUCLEOTIDE BINDING PROTEIN 2) (REPRESSOR OF TAMOXIFEN TRANSCRIPTIONAL ACTIVITY). [SWISSPROT;Acc:O43251] 1.55794 0.27250536
0.424679 1760 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] 1.79432 0.236679634
0.424703 719 ARPC5L 1.60405 0.264769178
0.425718 229 KIF2A KINESIN-LIKE PROTEIN KIF2 (KINESIN-2) (HK2). [SWISSPROT;Acc:O00139] 1.34686 0.31608185
0.427194 1383 UBQLN4 ATAXIN-1 UBIQUITIN-LIKE INTERACTING PROTEIN. [RefSeq;Acc:NM_020131] 1.74675 0.244565049
0.427564 778 ARPC2 ARP2/3 COMPLEX 34 KDA SUBUNIT (P34-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 2). [SWISSPROT;Acc:O15144] 1.62441 0.263211874
0.427985 911 LEF1 LYMPHOID ENHANCER BINDING FACTOR 1 (LEF-1) (T CELL-SPECIFIC TRANSCRIPTION FACTOR 1-ALPHA) (TCF1-ALPHA). [SWISSPROT;Acc:Q9UJU2] 1.6585 0.258055472
0.428065 2877 CKS2 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 2 (CKS-2). [SWISSPROT;Acc:P33552] 2.2717 0.188433772
0.42874 104 MICAL2 FLAVOPROTEIN OXIDOREDUCTASE MICAL2. [RefSeq;Acc:NM_014632] 1.147 0.373792502
0.429115 2421 FIP1L1 FIP1-LIKE 1; REARRANGED IN HYPEREOSINOPHILIA. [RefSeq;Acc:NM_030917] 1.96674 0.218185932
0.429285 159 no value FORMIN BINDING PROTEIN 3; FAS-LIGAND ASSOCIATED FACTOR 1; HUNTINGTIN-INTERACTING PROTEIN A; NY-REN-6 ANTIGEN. [RefSeq;Acc:NM_017892] 1.22508 0.350413851
0.429899 2754 ETFB ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT (BETA-ETF). [SWISSPROT;Acc:P38117] 2.11091 0.203655769
0.431627 668 FIGNL1 FIDGETIN-LIKE 1. [RefSeq;Acc:NM_022116] 1.61735 0.266872971
0.432107 2558 EEF2 ELONGATION FACTOR 2 (EF-2). [SWISSPROT;Acc:P13639] 2.01624 0.214313276
0.433722 105 VAV2 VAV-2 PROTEIN. [SWISSPROT;Acc:P52735] 1.16696 0.371668266
0.434898 1912 AK2 "ADENYLATE KINASE ISOENZYME 2, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P54819]" 1.87377 0.232097856
0.437521 2355 MRPS2 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S2 (MRP-S2) (CGI-91). [SWISSPROT;Acc:Q9Y399] 1.98545 0.220363646
0.43784 166 NCBP2 20 KDA NUCLEAR CAP BINDING PROTEIN (NCBP 20 KDA SUBUNIT) (CBP20) (NCBP INTERACTING PROTEIN 1) (NIP1). [SWISSPROT;Acc:P52298] 1.28032 0.341977006
0.438432 2684 PAPOLA POLY(A) POLYMERASE ALPHA (EC 2.7.7.19) (PAP) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE ALPHA) (FRAGMENT). [SWISSPROT;Acc:P51003] 2.10446 0.20833468
0.439158 14 NFYB 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] 0.912166 0.481445263
0.439273 2715 SLC27A3 SOLUTE CARRIER FAMILY 27 MEMBER 3; FATTY ACID TRANSPORT PROTEIN 3. [RefSeq;Acc:NM_024330] 2.11862 0.207339211
0.441621 451 XAB2 XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7] 1.59982 0.27604418
0.443267 2447 HARS2 HISTIDYL-TRNA SYNTHETASE HOMOLOG (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE HOMOLOG) (HISRS). [SWISSPROT;Acc:P49590] 2.0418 0.21709619
0.443276 535 TNPO1 IMPORTIN BETA-2 SUBUNIT (KARYOPHERIN BETA-2 SUBUNIT) (TRANSPORTIN) (M9 REGION INTERACTION PROTEIN) (MIP). [SWISSPROT;Acc:Q92973] 1.63446 0.271206392
0.445085 1999 METAP1 METHIONINE AMINOPEPTIDASE 1 (EC 3.4.11.18) (METAP 1) (MAP 1) (PEPTIDASE M 1). [SWISSPROT;Acc:P53582] 1.92889 0.230746699
2000 METAP2 METHIONINE AMINOPEPTIDASE 2 (EC 3.4.11.18) (METAP 2) (PEPTIDASE M 2) (INITIATION FACTOR 2 ASSOCIATED 67 KDA GLYCOPROTEIN) (P67) (P67EIF2). [SWISSPROT;Acc:P50579]

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/