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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final Gene measured Rank Hugo expected description
Results: HTML CSV LaTeX Showing element 101 to 150 of 3206 in total
final
measured
Rank
Hugo
expected
description
0.09222352 0.0728267 3106 NEUROD4 0.789676 NEUROGENIC DIFFERENTIATION FACTOR 4 (NEUROD4). [SWISSPROT;Acc:Q9HD90]
0.092223579 0.0744473 3105 NEUROD6 0.807248 NEUROGENIC DIFFERENTIATION FACTOR 6 (NEUROD6) (MY051 PROTEIN). [SWISSPROT;Acc:Q96NK8]
0.092223589 0.0749538 3104 CHD3 0.81274 CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 3 (CHD-3) (MI-2 AUTOANTIGEN 240 KDA PROTEIN) (MI2-ALPHA). [SWISSPROT;Acc:Q12873]
0.0922236 0.0917931 3103 NEUROD2 0.995332 NEUROGENIC DIFFERENTIATION FACTOR 2 (NEUROD2). [SWISSPROT;Acc:Q15784]
0.092223618 0.0752577 3102 NEUROD1 0.816035 NEUROGENIC DIFFERENTIATION FACTOR 1 (NEUROD1) (NEUROD). [SWISSPROT;Acc:Q13562]
0.092223823 0.247158 3101 CDK2AP2 2.67998 DOC-1 RELATED PROTEIN (DOC-1R). [SWISSPROT;Acc:O75956]
0.093016709 0.0506529 3100 DGCR14 0.544557 DGCR14 PROTEIN (DIGEORGE SYNDROME CRITICAL REGION 14) (ES2 PROTEIN). [SWISSPROT;Acc:Q96DF8]
0.094552115 0.063706 3099 TCP1 0.673766 "T-COMPLEX PROTEIN 1, ALPHA SUBUNIT (TCP-1-ALPHA) (CCT-ALPHA). [SWISSPROT;Acc:P17987]"
0.094589031 0.112123 3098 TIPRL 1.18537 CG9578-LIKE; YEAST YPR037W AND WORM C02C2.6 PREDICTED PROTEINS-LIKE. [RefSeq;Acc:NM_152902]
0.097185692 0.0570584 3096 CACNG8 0.587107 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-8 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-8 SUBUNIT). [SWISSPROT;Acc:Q8WXS5]
3097 CACNG3 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-3 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-3 SUBUNIT). [SWISSPROT;Acc:O60359]
0.097186119 0.0571433 3095 CACNG2 0.587978 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT). [SWISSPROT;Acc:Q9Y698]
0.097187514 0.0573556 3094 CACNG4 0.590154 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-4 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-4 SUBUNIT). [SWISSPROT;Acc:Q9UBN1]
0.09727581 0.0760798 3093 CACNG5 0.782104 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-5 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-5 SUBUNIT). [SWISSPROT;Acc:Q9UF02]
0.097635809 0.048624 3089 TM4SF19 0.498014
3090 no value METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396]
3091 METTL2A
3092 FZR1 FZR1 PROTEIN; FIZZY-RELATED PROTEIN; CDC20-LIKE 1B. [RefSeq;Acc:NM_016263]
0.097635942 0.587123 3088 DYNLT1 6.01339 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763]
0.097635972 0.038802 3087 FAM20A 0.397415
0.09763599 0.0398596 3086 PCSK5 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]
0.099462462 0.0586001 3085 DNASE2B 0.589168 DEOXYRIBONUCLEASE II BETA ISOFORM 1 PRECURSOR; DEOXYRIBONUCLEASE II BETA; ENDONUCLEASE DLAD. [RefSeq;Acc:NM_021233]
0.09970749 0.0979655 3084 GNB3 0.982529 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 3 (TRANSDUCIN BETA CHAIN 3). [SWISSPROT;Acc:P16520]
0.099867935 0.174683 3083 HOMER2 1.74914 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 2; HOMER HOMOLOG 3 (DROSOPHILA). [RefSeq;Acc:NM_004839]"
0.09991622 0.0558136 3082 COQ7 0.558604 UBIQUINONE BIOSYNTHESIS PROTEIN COQ7 HOMOLOG (COENZYME Q BIOSYNTHESIS PROTEIN 7 HOMOLOG) (TIMING PROTEIN CLK-1 HOMOLOG). [SWISSPROT;Acc:Q99807]
0.099937142 0.0454705 3081 CPA6 0.454991 CARBOXYPEPTIDASE B PRECURSOR. [RefSeq;Acc:NM_020361]
0.09993762 0.0451789 3080 CPA3 0.452071 MAST CELL CARBOXYPEPTIDASE A PRECURSOR (EC 3.4.17.1) (MC-CPA) (CARBOXYPEPTIDASE A3). [SWISSPROT;Acc:P15088]
0.09993858 0.0444208 3079 CPB2 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]
0.099939871 0.137954 3078 HOMER1 1.38037 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 1B. [RefSeq;Acc:NM_004272]"
0.099954583 0.13205 3077 HOMER3 1.3211 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 3. [RefSeq;Acc:NM_004838]"
0.103196836 0.102521 3076 TOB1 0.993451 TOB1 PROTEIN (TRANSDUCER OF ERBB-2 1). [SWISSPROT;Acc:P50616]
0.10319696 0.083343 3075 TOB2 0.807611 TOB2 PROTEIN (TRANSDUCER OF ERBB-2 2). [SWISSPROT;Acc:Q14106]
0.103196964 0.129151 3074 CPEB3 1.2515 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3. [RefSeq;Acc:NM_014912]
0.103196984 0.0550688 3073 RASAL2 0.533628 RAS GTPASE-ACTIVATING PROTEIN NGAP (RAS PROTEIN ACTIVATOR LIKE 1). [SWISSPROT;Acc:Q9UJF2]
0.103197028 0.0659913 3072 DAB2IP 0.639469 DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552]
0.103197029 0.164494 3071 CPEB4 1.59398 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 4. [RefSeq;Acc:NM_030627]
0.103197055 0.0365299 3070 C1orf156 0.353982
0.103197093 0.0533885 3069 no value 0.517345
0.103205275 0.167175 3068 GNB5 1.61983 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 5 (TRANSDUCIN BETA CHAIN 5). [SWISSPROT;Acc:O14775]
0.103512902 0.156084 3067 ATG4A 1.50787 CYSTEINE ENDOPEPTIDASE AUT-LIKE 2 ISOFORM A; AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2; AUTOPHAGIN 2. [RefSeq;Acc:NM_052936]
0.103560389 0.0670742 3066 MAP1LC3B 0.647682 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8]
0.103561168 0.0764589 3065 MAP1LC3A 0.738297 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A (MAP1A/MAP1B LC3 A) (MAP1A/1B LIGHT CHAIN 3 A). [SWISSPROT;Acc:Q9H492]
0.103620028 0.126175 3064 ATG4B 1.21767 CYSTEINE ENDOPEPTIDASE AUT-LIKE ISOFORM B. [RefSeq;Acc:NM_178326]
0.105304256 0.18745 3063 GNB4 1.78008 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 4 (TRANSDUCIN BETA CHAIN 4). [SWISSPROT;Acc:Q9HAV0]
0.105394906 0.204288 3062 CCT5 1.93831 "T-COMPLEX PROTEIN 1, EPSILON SUBUNIT (TCP-1-EPSILON) (CCT-EPSILON). [SWISSPROT;Acc:P48643]"
0.105426545 0.0510974 3060 GNAI1 0.484673 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04898]"
3061 GNAI3 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(K), ALPHA SUBUNIT (G(I) ALPHA-3). [SWISSPROT;Acc:P08754]"
0.105432626 0.0485629 3059 GNAI2 0.460606 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-2 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04899]"
0.105443556 0.0446932 3058 GNAT2 0.423859 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-2 SUBUNIT (TRANSDUCIN ALPHA-2 CHAIN). [SWISSPROT;Acc:P19087]"
0.105444244 0.044407 3057 GNAT1 0.421142 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1 SUBUNIT (TRANSDUCIN ALPHA-1 CHAIN). [SWISSPROT;Acc:P11488]"

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/