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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Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 3051 to 3100 of 3206 in total
Rank
expected
description
measured
Hugo
final
3051 1.92471 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 1 (TRANSDUCIN BETA CHAIN 1). [SWISSPROT;Acc:P04901] 0.204254 GNB1 0.106121961
3052 0.857352 "BASIC HELIX-LOOP-HELIX DOMAIN CONTAINING, CLASS B, 5; TRINUCLEOTIDE REPEAT CONTAINING 20. [RefSeq;Acc:NM_152414]" 0.090943 BHLHB5 0.106074285
3053 0.65236 BA305P22.3 (BREAST CARCINOMA AMPLIFIED SEQUENCE 4). [SPTREMBL;Acc:Q8NDY6] 0.0691801 BHLHB4 0.106045895
3054 0.371714 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Y), ALPHA SUBUNIT (ALPHA-11). [SWISSPROT;Acc:P29992]" 0.0392019 GNA11 0.105462533
3055 0.375337 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Q), ALPHA SUBUNIT. [SWISSPROT;Acc:P50148]" 0.0395834 GNAQ 0.105460959
3056 0.415448 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Z), ALPHA SUBUNIT (G(X) ALPHA CHAIN) (GZ-ALPHA). [SWISSPROT;Acc:P19086]" 0.0438075 GNAZ 0.10544641
3057 0.421142 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1 SUBUNIT (TRANSDUCIN ALPHA-1 CHAIN). [SWISSPROT;Acc:P11488]" 0.044407 GNAT1 0.105444244
3058 0.423859 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-2 SUBUNIT (TRANSDUCIN ALPHA-2 CHAIN). [SWISSPROT;Acc:P19087]" 0.0446932 GNAT2 0.105443556
3059 0.460606 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-2 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04899]" 0.0485629 GNAI2 0.105432626
3060 0.484673 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04898]" 0.0510974 GNAI1 0.105426545
3061 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(K), ALPHA SUBUNIT (G(I) ALPHA-3). [SWISSPROT;Acc:P08754]" GNAI3
3062 1.93831 "T-COMPLEX PROTEIN 1, EPSILON SUBUNIT (TCP-1-EPSILON) (CCT-EPSILON). [SWISSPROT;Acc:P48643]" 0.204288 CCT5 0.105394906
3063 1.78008 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 4 (TRANSDUCIN BETA CHAIN 4). [SWISSPROT;Acc:Q9HAV0] 0.18745 GNB4 0.105304256
3064 1.21767 CYSTEINE ENDOPEPTIDASE AUT-LIKE ISOFORM B. [RefSeq;Acc:NM_178326] 0.126175 ATG4B 0.103620028
3065 0.738297 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A (MAP1A/MAP1B LC3 A) (MAP1A/1B LIGHT CHAIN 3 A). [SWISSPROT;Acc:Q9H492] 0.0764589 MAP1LC3A 0.103561168
3066 0.647682 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8] 0.0670742 MAP1LC3B 0.103560389
3067 1.50787 CYSTEINE ENDOPEPTIDASE AUT-LIKE 2 ISOFORM A; AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2; AUTOPHAGIN 2. [RefSeq;Acc:NM_052936] 0.156084 ATG4A 0.103512902
3068 1.61983 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 5 (TRANSDUCIN BETA CHAIN 5). [SWISSPROT;Acc:O14775] 0.167175 GNB5 0.103205275
3069 0.517345 0.0533885 no value 0.103197093
3070 0.353982 0.0365299 C1orf156 0.103197055
3071 1.59398 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 4. [RefSeq;Acc:NM_030627] 0.164494 CPEB4 0.103197029
3072 0.639469 DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552] 0.0659913 DAB2IP 0.103197028
3073 0.533628 RAS GTPASE-ACTIVATING PROTEIN NGAP (RAS PROTEIN ACTIVATOR LIKE 1). [SWISSPROT;Acc:Q9UJF2] 0.0550688 RASAL2 0.103196984
3074 1.2515 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3. [RefSeq;Acc:NM_014912] 0.129151 CPEB3 0.103196964
3075 0.807611 TOB2 PROTEIN (TRANSDUCER OF ERBB-2 2). [SWISSPROT;Acc:Q14106] 0.083343 TOB2 0.10319696
3076 0.993451 TOB1 PROTEIN (TRANSDUCER OF ERBB-2 1). [SWISSPROT;Acc:P50616] 0.102521 TOB1 0.103196836
3077 1.3211 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 3. [RefSeq;Acc:NM_004838]" 0.13205 HOMER3 0.099954583
3078 1.38037 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 1B. [RefSeq;Acc:NM_004272]" 0.137954 HOMER1 0.099939871
3079 0.444481 PLASMA CARBOXYPEPTIDASE B2 ISOFORM A PREPROPROTEIN; CARBOXYPEPTIDASE U; THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR; CARBOXYPEPTIDASE B-LIKE PROTEIN; THROMBIN-ACTIVABLE FIBRINOLYSIS INHIBITOR. [RefSeq;Acc:NM_001872] 0.0444208 CPB2 0.09993858
3080 0.452071 MAST CELL CARBOXYPEPTIDASE A PRECURSOR (EC 3.4.17.1) (MC-CPA) (CARBOXYPEPTIDASE A3). [SWISSPROT;Acc:P15088] 0.0451789 CPA3 0.09993762
3081 0.454991 CARBOXYPEPTIDASE B PRECURSOR. [RefSeq;Acc:NM_020361] 0.0454705 CPA6 0.099937142
3082 0.558604 UBIQUINONE BIOSYNTHESIS PROTEIN COQ7 HOMOLOG (COENZYME Q BIOSYNTHESIS PROTEIN 7 HOMOLOG) (TIMING PROTEIN CLK-1 HOMOLOG). [SWISSPROT;Acc:Q99807] 0.0558136 COQ7 0.09991622
3083 1.74914 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 2; HOMER HOMOLOG 3 (DROSOPHILA). [RefSeq;Acc:NM_004839]" 0.174683 HOMER2 0.099867935
3084 0.982529 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 3 (TRANSDUCIN BETA CHAIN 3). [SWISSPROT;Acc:P16520] 0.0979655 GNB3 0.09970749
3085 0.589168 DEOXYRIBONUCLEASE II BETA ISOFORM 1 PRECURSOR; DEOXYRIBONUCLEASE II BETA; ENDONUCLEASE DLAD. [RefSeq;Acc:NM_021233] 0.0586001 DNASE2B 0.099462462
3086 0.408247 PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 5 PRECURSOR (EC 3.4.21.-) (PROPROTEIN CONVERTASE PC5) (SUBTILISIN/KEXIN-LIKE PROTEASE PC5) (CONVERTASE PC5) (PC6) (HPC6). [SWISSPROT;Acc:Q92824] 0.0398596 PCSK5 0.09763599
3087 0.397415 0.038802 FAM20A 0.097635972
3088 6.01339 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763] 0.587123 DYNLT1 0.097635942
3089 0.498014 0.048624 TM4SF19 0.097635809
3090 METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396] no value
3091 METTL2A
3092 FZR1 PROTEIN; FIZZY-RELATED PROTEIN; CDC20-LIKE 1B. [RefSeq;Acc:NM_016263] FZR1
3093 0.782104 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-5 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-5 SUBUNIT). [SWISSPROT;Acc:Q9UF02] 0.0760798 CACNG5 0.09727581
3094 0.590154 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-4 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-4 SUBUNIT). [SWISSPROT;Acc:Q9UBN1] 0.0573556 CACNG4 0.097187514
3095 0.587978 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT). [SWISSPROT;Acc:Q9Y698] 0.0571433 CACNG2 0.097186119
3096 0.587107 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-8 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-8 SUBUNIT). [SWISSPROT;Acc:Q8WXS5] 0.0570584 CACNG8 0.097185692
3097 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-3 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-3 SUBUNIT). [SWISSPROT;Acc:O60359] CACNG3
3098 1.18537 CG9578-LIKE; YEAST YPR037W AND WORM C02C2.6 PREDICTED PROTEINS-LIKE. [RefSeq;Acc:NM_152902] 0.112123 TIPRL 0.094589031
3099 0.673766 "T-COMPLEX PROTEIN 1, ALPHA SUBUNIT (TCP-1-ALPHA) (CCT-ALPHA). [SWISSPROT;Acc:P17987]" 0.063706 TCP1 0.094552115
3100 0.544557 DGCR14 PROTEIN (DIGEORGE SYNDROME CRITICAL REGION 14) (ES2 PROTEIN). [SWISSPROT;Acc:Q96DF8] 0.0506529 DGCR14 0.093016709

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/