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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description Gene Rank expected Hugo measured final
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 3206 in total
description
Rank
expected
Hugo
measured
final
60S RIBOSOMAL PROTEIN L30. [SWISSPROT;Acc:P04645] 1971 0.767511 RPL30 0.177407 0.231145873
60S RIBOSOMAL PROTEIN L31. [SWISSPROT;Acc:P12947] 1842 0.803133 RPL31 0.187564 0.233540397
60S RIBOSOMAL PROTEIN L32. [SWISSPROT;Acc:P02433] 1927 3.09201 SNORA7A 0.716691 0.23178806
60S RIBOSOMAL PROTEIN L34. [SWISSPROT;Acc:P49207] 1956 0.165264 RPL34 0.0382183 0.231256051
60S RIBOSOMAL PROTEIN L35. [SWISSPROT;Acc:P42766] 1942 5.59596 RPL35 1.29605 0.231604586
60S RIBOSOMAL PROTEIN L37 (G1.16). [SWISSPROT;Acc:P02403] 1684 0.100146 RPL37 0.0238444 0.238096379
60S RIBOSOMAL PROTEIN L39. [SWISSPROT;Acc:P02404] 1841 0.803133 no value 0.187564 0.233540397
60S RIBOSOMAL PROTEIN L4 (L1). [SWISSPROT;Acc:P36578] 1710 3.49797 RPL4 0.83123 0.237632112
60S RIBOSOMAL PROTEIN L5. [SWISSPROT;Acc:P46777] 1968 6.13294 RPL5 1.41778 0.231174608
60S RIBOSOMAL PROTEIN L7. [SWISSPROT;Acc:P18124] 2166 1.35464 no value 0.30758 0.227056635
60S RIBOSOMAL PROTEIN L8. [SWISSPROT;Acc:P25120] 2868 0.393799 RPL8 0.0744045 0.188940297
60S RIBOSOMAL PROTEIN L9. [SWISSPROT;Acc:P32969] 1814 3.36493 no value 0.788679 0.234381993
65 KDA YES-ASSOCIATED PROTEIN (YAP65). [SWISSPROT;Acc:P46937] 463 0.315578 YAP1 0.0869671 0.275580364
9 KDA PROTEIN. [SWISSPROT;Acc:P13994] 462 CCDC130
A KINDRED OF IGLON. [RefSeq;Acc:NM_173808] 802 0.379834 NEGR1 0.099521 0.262011826
A-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (A-RAF-1) (PROTO-ONCOGENE PKS). [SWISSPROT;Acc:P10398] 2956 1.48145 ARAF 0.218717 0.147637112
AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421] 1651 0.142333 ADCK1 0.0340138 0.238973393
AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853] 1652 ADCK2
AARF DOMAIN CONTAINING KINASE 4. [RefSeq;Acc:NM_024876] 1653 0.115005 ADCK4 0.0274831 0.238973088
ABHYDROLASE DOMAIN CONTAINING PROTEIN 2 (PROTEIN PHPS1-2). [SWISSPROT;Acc:P08910] 546 0.183589 ABHD2 0.0497647 0.271065805
ABL-INTERACTOR 2; ABL-INTERACTING PROTEIN 1 (SH3-CONTAINING PROTEIN); ABL BINDING PROTEIN 3; ARG PROTEIN TYROSINE KINASE-BINDING PROTEIN; ABL-INTERACTOR PROTEIN 2B; SIMILAR TO SPECTRIN SH3 DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_005759] 500 1.14976 ABI2 0.315262 0.274198094
ACETYL-COA CARBOXYLASE 1 (EC 6.4.1.2) (ACC-ALPHA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:Q13085] 2757 5.26987 ACACA 1.06806 0.202672931
ACETYL-COA CARBOXYLASE 2 (EC 6.4.1.2) (ACC-BETA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:O00763] 2762 4.63429 ACACB 0.938896 0.202597593
ACID CERAMIDASE PRECURSOR (EC 3.5.1.23) (ACYLSPHINGOSINE DEACYLASE) (N-ACYLSPHINGOSINE AMIDOHYDROLASE) (AC) (PUTATIVE 32 KDA HEART PROTEIN) (PHP32). [SWISSPROT;Acc:Q13510] 1618 0.35015 ASAH1 0.083902 0.239617307
ACRC PROTEIN; PUTATIVE NUCLEAR PROTEIN. [RefSeq;Acc:NM_052957] 1025 0.256212 ACRC 0.0649343 0.25343973
ACTIN BINDING LIM PROTEIN 2. [RefSeq;Acc:NM_032432] 71 0.152757 ABLIM2 0.0620387 0.406126724
ACTIN-BINDING LIM PROTEIN 1 ISOFORM A; LIM ACTIN-BINDING PROTEIN 1; LIMATIN; ACTIN-BINDING LIM PROTEIN. [RefSeq;Acc:NM_002313] 80 0.187896 ABLIM1 0.0763094 0.406125729
ACTIN-LIKE PROTEIN 2 (ACTIN-RELATED PROTEIN 2). [SWISSPROT;Acc:O15142] 729 1.47645 ACTR2 0.390781 0.264676081
ACTIN-LIKE PROTEIN 3 (ACTIN-RELATED PROTEIN 3) (ACTIN-2). [SWISSPROT;Acc:P32391] 723 1.99819 ACTR3 0.528875 0.264677033
ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1A (SOP2-LIKE PROTEIN). [SWISSPROT;Acc:Q92747] 724 1.3445 ARPC1A 0.355858 0.264676832
ACTIVATED P21CDC42HS KINASE. [RefSeq;Acc:NM_005781] 2294 0.145189 TNK2 0.0322816 0.222341913
ACTIVATOR OF BASAL TRANSCRIPTION 1; TATA-BINDING PROTEIN-BINDING PROTEIN; BASAL TRANSCRIPTIONAL ACTIVATOR. [RefSeq;Acc:NM_013375] 987 0.136958 ABT1 0.0349473 0.255168008
ACTIVATOR OF CAMP-RESPONSIVE ELEMENT MODULATOR (CREM) IN TESTIS; LIM PROTEIN ACT. [RefSeq;Acc:NM_020482] 2726 2.24591 FHL5 0.462047 0.20572819
AD24 PROTEIN. [RefSeq;Acc:NM_022451] 1334 1.18321 NOC3L 0.290237 0.24529627
ADAMTS-9 PRECURSOR (EC 3.4.24.-) (A DISINTEGRIN AND METALLOPROTEINASE WITH THROMBOSPONDIN MOTIFS 9) (ADAM-TS 9) (ADAM-TS9). [SWISSPROT;Acc:Q9P2N4] 1819 0.326867 ADAMTS9 0.0765741 0.234266842
ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT (BETA-ADAPTIN 1) (ADAPTOR PROTEIN COMPLEX AP-1 BETA-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN BETA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 BETA LARGE CHAIN). [SWISSPROT;Acc:Q10567] 1164 1.25482 AP1B1 0.313086 0.249506702
ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT (GAMMA-ADAPTIN) (ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN GAMMA-1 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN). [SWISSPROT;Acc:O43747] 1162 0.925078 AP1G1 0.230865 0.24956274
ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 2 SUBUNIT (GAMMA2-ADAPTIN) (ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-2 SUBUNIT) (G2AD). [SWISSPROT;Acc:O75843] 1160 0.774489 JPH4 0.193284 0.24956326
ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT (SIGMA-ADAPTIN 1A) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1A SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1A SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1A SMALL CHAIN) (CLATHRIN COAT ASSEMBLY PROT 1163 0.456524 AP1S1 0.113931 0.249561907
ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1B SUBUNIT (SIGMA-ADAPTIN 1B) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1B SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1B SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1B SMALL CHAIN) (SIGMA 1B SUBUNIT OF AP-1 CL 1161 0.512059 no value 0.127791 0.249563039
ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1C SUBUNIT (SIGMA-ADAPTIN 1C) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1C SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1C SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1C SMALL CHAIN) (SIGMA 1C SUBUNIT OF AP-1 CL 1159 0.22389 AP1S3 0.0558748 0.249563625
ADAPTER-RELATED PROTEIN COMPLEX 2 BETA 1 SUBUNIT (BETA-ADAPTIN) (PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN) (AP105B). [SWISSPROT;Acc:P21851] 1158 1.17572 AP2B1 0.29348 0.249617256
ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 1 SUBUNIT (BETA-ADAPTIN 3A) (AP-3 COMPLEX BETA-3A SUBUNIT) (BETA-3A-ADAPTIN). [SWISSPROT;Acc:O00203] 2882 0.225994 AP3B1 0.0416917 0.184481446
ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 2 SUBUNIT (BETA-ADAPTIN 3B) (AP-3 COMPLEX BETA-3B SUBUNIT) (BETA-3B-ADAPTIN) (NEURON-SPECIFIC VESICLE COAT PROTEIN BETA-NAP). [SWISSPROT;Acc:Q13367] 2881 0.278146 no value 0.0513128 0.184481531
ADAPTER-RELATED PROTEIN COMPLEX 3 MU 1 SUBUNIT (MU-ADAPTIN 3A) (AP-3 ADAPTER COMPLEX MU3A SUBUNIT). [SWISSPROT;Acc:Q9Y2T2] 2309 0.732966 AP3M1 0.162756 0.222051227
ADAPTER-RELATED PROTEIN COMPLEX 3 MU 2 SUBUNIT (CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG 2) (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG 2) (GOLGI ADAPTOR AP-1 47 KDA PROTEIN HOMOLOG 2) (HA1 47 KDA SUBUNIT HOMOLOG 2) (CLATHRIN ASSEMBLY PROTEIN ASSEMB 2312 0.828397 AP3M2 0.183942 0.22204571
ADAPTOR-ASSOCIATED KINASE 1. [RefSeq;Acc:NM_014911] 423 0.60766 AAK1 0.168547 0.277370569
ADENINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.7) (APRT). [SWISSPROT;Acc:P07741] 1780 1.16418 no value 0.273997 0.235356216
ADENOSINE KINASE (EC 2.7.1.20) (AK) (ADENOSINE 5'-PHOSPHOTRANSFERASE). [SWISSPROT;Acc:P55263] 2171 0.691417 ADK 0.156968 0.227023634
ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) (S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:P23526] 2335 0.605534 AHCY 0.133936 0.221186589

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/