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 description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 3058 to 3107 of 3206 in total
Rank
description
measured
expected
final
Hugo
3058 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-2 SUBUNIT (TRANSDUCIN ALPHA-2 CHAIN). [SWISSPROT;Acc:P19087]" 0.0446932 0.423859 0.105443556 GNAT2
3059 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-2 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04899]" 0.0485629 0.460606 0.105432626 GNAI2
3060 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04898]" 0.0510974 0.484673 0.105426545 GNAI1
3061 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(K), ALPHA SUBUNIT (G(I) ALPHA-3). [SWISSPROT;Acc:P08754]" GNAI3
3062 "T-COMPLEX PROTEIN 1, EPSILON SUBUNIT (TCP-1-EPSILON) (CCT-EPSILON). [SWISSPROT;Acc:P48643]" 0.204288 1.93831 0.105394906 CCT5
3063 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 4 (TRANSDUCIN BETA CHAIN 4). [SWISSPROT;Acc:Q9HAV0] 0.18745 1.78008 0.105304256 GNB4
3064 CYSTEINE ENDOPEPTIDASE AUT-LIKE ISOFORM B. [RefSeq;Acc:NM_178326] 0.126175 1.21767 0.103620028 ATG4B
3065 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A (MAP1A/MAP1B LC3 A) (MAP1A/1B LIGHT CHAIN 3 A). [SWISSPROT;Acc:Q9H492] 0.0764589 0.738297 0.103561168 MAP1LC3A
3066 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8] 0.0670742 0.647682 0.103560389 MAP1LC3B
3067 CYSTEINE ENDOPEPTIDASE AUT-LIKE 2 ISOFORM A; AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2; AUTOPHAGIN 2. [RefSeq;Acc:NM_052936] 0.156084 1.50787 0.103512902 ATG4A
3068 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 5 (TRANSDUCIN BETA CHAIN 5). [SWISSPROT;Acc:O14775] 0.167175 1.61983 0.103205275 GNB5
3069 0.0533885 0.517345 0.103197093 no value
3070 0.0365299 0.353982 0.103197055 C1orf156
3071 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 4. [RefSeq;Acc:NM_030627] 0.164494 1.59398 0.103197029 CPEB4
3072 DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552] 0.0659913 0.639469 0.103197028 DAB2IP
3073 RAS GTPASE-ACTIVATING PROTEIN NGAP (RAS PROTEIN ACTIVATOR LIKE 1). [SWISSPROT;Acc:Q9UJF2] 0.0550688 0.533628 0.103196984 RASAL2
3074 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3. [RefSeq;Acc:NM_014912] 0.129151 1.2515 0.103196964 CPEB3
3075 TOB2 PROTEIN (TRANSDUCER OF ERBB-2 2). [SWISSPROT;Acc:Q14106] 0.083343 0.807611 0.10319696 TOB2
3076 TOB1 PROTEIN (TRANSDUCER OF ERBB-2 1). [SWISSPROT;Acc:P50616] 0.102521 0.993451 0.103196836 TOB1
3077 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 3. [RefSeq;Acc:NM_004838]" 0.13205 1.3211 0.099954583 HOMER3
3078 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 1B. [RefSeq;Acc:NM_004272]" 0.137954 1.38037 0.099939871 HOMER1
3079 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 0.444481 0.09993858 CPB2
3080 MAST CELL CARBOXYPEPTIDASE A PRECURSOR (EC 3.4.17.1) (MC-CPA) (CARBOXYPEPTIDASE A3). [SWISSPROT;Acc:P15088] 0.0451789 0.452071 0.09993762 CPA3
3081 CARBOXYPEPTIDASE B PRECURSOR. [RefSeq;Acc:NM_020361] 0.0454705 0.454991 0.099937142 CPA6
3082 UBIQUINONE BIOSYNTHESIS PROTEIN COQ7 HOMOLOG (COENZYME Q BIOSYNTHESIS PROTEIN 7 HOMOLOG) (TIMING PROTEIN CLK-1 HOMOLOG). [SWISSPROT;Acc:Q99807] 0.0558136 0.558604 0.09991622 COQ7
3083 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 2; HOMER HOMOLOG 3 (DROSOPHILA). [RefSeq;Acc:NM_004839]" 0.174683 1.74914 0.099867935 HOMER2
3084 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 3 (TRANSDUCIN BETA CHAIN 3). [SWISSPROT;Acc:P16520] 0.0979655 0.982529 0.09970749 GNB3
3085 DEOXYRIBONUCLEASE II BETA ISOFORM 1 PRECURSOR; DEOXYRIBONUCLEASE II BETA; ENDONUCLEASE DLAD. [RefSeq;Acc:NM_021233] 0.0586001 0.589168 0.099462462 DNASE2B
3086 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 0.408247 0.09763599 PCSK5
3087 0.038802 0.397415 0.097635972 FAM20A
3088 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763] 0.587123 6.01339 0.097635942 DYNLT1
3089 0.048624 0.498014 0.097635809 TM4SF19
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 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-5 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-5 SUBUNIT). [SWISSPROT;Acc:Q9UF02] 0.0760798 0.782104 0.09727581 CACNG5
3094 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-4 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-4 SUBUNIT). [SWISSPROT;Acc:Q9UBN1] 0.0573556 0.590154 0.097187514 CACNG4
3095 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT). [SWISSPROT;Acc:Q9Y698] 0.0571433 0.587978 0.097186119 CACNG2
3096 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-8 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-8 SUBUNIT). [SWISSPROT;Acc:Q8WXS5] 0.0570584 0.587107 0.097185692 CACNG8
3097 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-3 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-3 SUBUNIT). [SWISSPROT;Acc:O60359] CACNG3
3098 CG9578-LIKE; YEAST YPR037W AND WORM C02C2.6 PREDICTED PROTEINS-LIKE. [RefSeq;Acc:NM_152902] 0.112123 1.18537 0.094589031 TIPRL
3099 "T-COMPLEX PROTEIN 1, ALPHA SUBUNIT (TCP-1-ALPHA) (CCT-ALPHA). [SWISSPROT;Acc:P17987]" 0.063706 0.673766 0.094552115 TCP1
3100 DGCR14 PROTEIN (DIGEORGE SYNDROME CRITICAL REGION 14) (ES2 PROTEIN). [SWISSPROT;Acc:Q96DF8] 0.0506529 0.544557 0.093016709 DGCR14
3101 DOC-1 RELATED PROTEIN (DOC-1R). [SWISSPROT;Acc:O75956] 0.247158 2.67998 0.092223823 CDK2AP2
3102 NEUROGENIC DIFFERENTIATION FACTOR 1 (NEUROD1) (NEUROD). [SWISSPROT;Acc:Q13562] 0.0752577 0.816035 0.092223618 NEUROD1
3103 NEUROGENIC DIFFERENTIATION FACTOR 2 (NEUROD2). [SWISSPROT;Acc:Q15784] 0.0917931 0.995332 0.0922236 NEUROD2
3104 CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 3 (CHD-3) (MI-2 AUTOANTIGEN 240 KDA PROTEIN) (MI2-ALPHA). [SWISSPROT;Acc:Q12873] 0.0749538 0.81274 0.092223589 CHD3
3105 NEUROGENIC DIFFERENTIATION FACTOR 6 (NEUROD6) (MY051 PROTEIN). [SWISSPROT;Acc:Q96NK8] 0.0744473 0.807248 0.092223579 NEUROD6
3106 NEUROGENIC DIFFERENTIATION FACTOR 4 (NEUROD4). [SWISSPROT;Acc:Q9HD90] 0.0728267 0.789676 0.09222352 NEUROD4
3107 CHROMODOMAIN HELICASE DNA BINDING PROTEIN 5. [RefSeq;Acc:NM_015557] 0.0762705 0.827018 0.092223507 CHD5

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/