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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Hugo description Rank Gene final expected measured
Results: HTML CSV LaTeX Showing element 601 to 650 of 3206 in total
Hugo
description
Rank
final
expected
measured
BAG1 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-1 (BCL-2 BINDING ATHANOGENE- 1) (BAG-1) (GLUCOCORTICOID RECEPTOR-ASSOCIATED PROTEIN RAP46). [SWISSPROT;Acc:Q99933] 1380 0.244646912 0.819994 0.200609
BAG2 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-2. [SWISSPROT;Acc:O95816] 1064 0.252635836 0.608346 0.15369
BAG3 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-3 (BCL-2 BINDING ATHANOGENE- 3) (BAG-3) (BCL-2-BINDING PROTEIN BIS) (DOCKING PROTEIN CAIR-1). [SWISSPROT;Acc:O95817] 1300 0.245785127 0.396904 0.0975531
BAIAP3 BAI1-ASSOCIATED PROTEIN 3; BAI-ASSOCIATED PROTEIN 3. [RefSeq;Acc:NM_003933] 656 0.26758858 0.0901025 0.0241104
BARD1 BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1 (BARD-1). [SWISSPROT;Acc:Q99728] 664 0.267067067 0.45954 0.122728
BARX1 HOMEOBOX PROTEIN BARH-LIKE 1. [SWISSPROT;Acc:Q9HBU1] 869 0.260266579 0.537326 0.139848
BARX2 HOMEOBOX PROTEIN BARH-LIKE 2. [SWISSPROT;Acc:Q9UMQ3] 875 0.260265287 0.419545 0.109193
BBOX1 "GAMMA-BUTYROBETAINE,2-OXOGLUTARATE DIOXYGENASE (EC 1.14.11.1) (GAMMA-BUTYROBETAINE HYDROXYLASE) (GAMMA-BBH). [SWISSPROT;Acc:O75936]" 1082 0.252073003 0.203883 0.0513934
BBS7 BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824] 742 0.264498255 0.145821 0.0385694
BCAR1 CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGEN RESISTANCE 1 PROTEIN). [SWISSPROT;Acc:P56945] 190 0.326398066 0.524421 0.17117
BCAR3 BREAST CANCER ANTIESTROGEN RESISTANCE 3. [RefSeq;Acc:NM_003567] 188 0.328882929 0.480256 0.157948
BCAS2 "BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]" 519 0.272249901 0.139495 0.0379775
BCAT1 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, CYTOSOLIC (EC 2.6.1.42) (BCAT(C)) (ECA39 PROTEIN). [SWISSPROT;Acc:P54687]" 1461 0.243046313 1.94005 0.471522
BCAT2 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]" 1452 0.243340427 1.57878 0.384181
BCCIP BRCA2 AND CDKN1A-INTERACTING PROTEIN ISOFORM BCCIPALPHA; BRCA2 AND CDKN1A-INTERACTING PROTEIN; CDK INHIBITOR P21 BINDING PROTEIN; BCCIPALPHA; BCCIPBETA; TOK-1ALPHA; TOK-1BETA. [RefSeq;Acc:NM_016567] 2015 0.230624509 0.0725001 0.0167203
BCKDHB "2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN) (BCKDH E1-BETA). [SWISSPROT;Acc:P21953]" 432 0.277366829 0.63809 0.176985
BCKDK "[3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE, MITOCHONDRIAL PRECURSOR (EC 2.7.1.115) (BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE) (BCKDHKIN) (BCKD-KINASE). [SWISSPROT;Acc:O14874]" 2537 0.21465603 5.29857 1.13737
BCL3 B-CELL LYMPHOMA 3-ENCODED PROTEIN (BCL-3 PROTEIN). [SWISSPROT;Acc:P20749] 1545 0.241816959 1.75491 0.424367
BCL6 B-CELL LYMPHOMA 6 PROTEIN (BCL-6) (ZINC FINGER PROTEIN 51) (LAZ-3 PROTEIN) (BCL-5). [SWISSPROT;Acc:P41182] 734 0.264650557 0.328537 0.0869475
BCL6B "B-CELL CLL/LYMPHOMA 6, MEMBER B (ZINC FINGER PROTEIN); ZINC FINGER PROTEIN 62. [RefSeq;Acc:NM_181844]" 737 0.264650434 0.261825 0.0692921
BCMO1 "BETA-CAROTENE 15, 15'-DIOXYGENASE; BETA-CAROTENE 15,15'-MONOOXYGENASE. [RefSeq;Acc:NM_017429]" 283 0.301810307 0.182179 0.0549835
BECN1 BECLIN 1 (COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN) (PROTEIN GT197). [SWISSPROT;Acc:Q14457] 2063 0.229610649 0.20547 0.0471781
BHLHB4 BA305P22.3 (BREAST CARCINOMA AMPLIFIED SEQUENCE 4). [SPTREMBL;Acc:Q8NDY6] 3053 0.106045895 0.65236 0.0691801
BHLHB5 "BASIC HELIX-LOOP-HELIX DOMAIN CONTAINING, CLASS B, 5; TRINUCLEOTIDE REPEAT CONTAINING 20. [RefSeq;Acc:NM_152414]" 3052 0.106074285 0.857352 0.090943
BIRC5 BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5 (APOPTOSIS INHIBITOR SURVIVIN) (APOPTOSIS INHIBITOR 4). [SWISSPROT;Acc:O15392] 756 0.264139825 0.636394 0.168097
BLOC1S1 GCN5-LIKE PROTEIN 1 (RT14 PROTEIN). [SWISSPROT;Acc:P78537] 1564 0.241128877 0.927081 0.223546
BOLA2B MY016 PROTEIN. [SPTREMBL;Acc:Q9H3K6] 2438 0.21722893 0.563645 0.12244
BOP1 BLOCK OF PROLIFERATION 1. [SWISSPROT;Acc:Q14137] 1265 0.246895277 3.53236 0.872123
BPI BACTERICIDAL PERMEABILITY-INCREASING PROTEIN PRECURSOR (BPI) (CAP 57). [SWISSPROT;Acc:P17213] 2159 0.227244147 0.0865184 0.0196608
BPIL2 2157 0.227245148 0.0622988 0.0141571
BRAF B-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (P94) (V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1). [SWISSPROT;Acc:P15056] 2950 0.147730689 1.90278 0.281099
BRCA1 BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN. [SWISSPROT;Acc:P38398] 785 0.262562329 0.432583 0.11358
BRD2 BROMODOMAIN-CONTAINING PROTEIN 2 (RING3 PROTEIN) (O27.1.1). [SWISSPROT;Acc:P25440] 537 0.271083457 0.390223 0.105783
BRD3 BROMODOMAIN-CONTAINING PROTEIN 3 (RING3-LIKE PROTEIN). [SWISSPROT;Acc:Q15059] 536 0.271112334 0.450566 0.122154
BRD4 BROMODOMAIN-CONTAINING PROTEIN 4 (HUNK1 PROTEIN). [SWISSPROT;Acc:O60885] 538 0.27107837 0.534019 0.144761
BRD7 BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [RefSeq;Acc:NM_013263] 2460 0.216714815 1.22885 0.26631
BRD9 2465 0.21671046 0.970087 0.210228
BRDT TESTIS-SPECIFIC BROMODOMAIN PROTEIN. [RefSeq;Acc:NM_001726] 544 0.27107069 0.36752 0.0996239
BRF1 "TRANSCRIPTION FACTOR IIIB 90 KDA SUBUNIT (TFIIIB90) (HTFIIIB90) (B- RELATED FACTOR 1) (HBRF) (TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE III, SUBUNIT 2) (TAF3B2). [SWISSPROT;Acc:Q92994]" 257 0.311284767 0.121057 0.0376832
BRP44 BRAIN PROTEIN 44. [SWISSPROT;Acc:O95563] 3010 0.122065817 0.163819 0.0199967
BRPF1 TUBULIN TYROSINE LIGASE-LIKE PROTEIN HOTTL (HQP0207). [SWISSPROT;Acc:Q9Y4R7] 678 0.265924938 2.04792 0.544593
BSCL2 2136 0.227977219 0.276021 0.0629265
BTAF1 TBP-ASSOCIATED FACTOR 172 (TAF-172) (TAF(II)170). [SWISSPROT;Acc:O14981] 1238 0.247698569 1.14255 0.283008
BTBD9 563 0.270811779 0.850576 0.230346
BTF3 TRANSCRIPTION FACTOR BTF3 (RNA POLYMERASE B TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P20290] 239 0.313139235 2.35516 0.737493
BTF3L4 238 0.313861137 2.82668 0.887185
BUB1B MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA (EC 2.7.1.-) (HBUBR1) (MAD3/BUB1-RELATED PROTEIN KINASE) (MITOTIC CHECKPOINT KINASE MAD3L). [SWISSPROT;Acc:O60566] 1132 0.250506991 0.466478 0.116856
BUB3 MITOTIC CHECKPOINT PROTEIN BUB3. [SWISSPROT;Acc:O43684] 1636 0.239179313 0.64312 0.153821
BUD13 1295 0.245899107 0.163123 0.0401118
BYSL BYSTIN. [SWISSPROT;Acc:Q13895] 1591 0.240285409 3.26689 0.784986

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/